Let's see if I can shed some light on this. Updated to Chocolatey 0.9.10-beta1 to see if this behaviour disappears, sadly it didn't. To puppet runs back to back will result in the file getting replaced both runs. There are no "manual" chocolatey interference during those runs as they are back to back, allthough I notice quite som action in my chocolatey.log durring those runs. I'm a little uncertain if that is the normal behaviour or not as I haven't monitored this file before this issue occured. I asked my puppet master right now and he had the feeling this surfaced when we moved from agent version 3.8.1 to 3.8.3, I'm not 100% with him on that as I know there where some server updates in the same time frame. Anyhow, logs are fun so I'm gonna give you the 225 rows it logs during the normal puppet run that might cast a light on whether chocolatey or puppet is the bad guy....
chocolatey.log:
2015-10-08 08:47:56,795 [DEBUG] - Configured chocolatey.infrastructure.logging.log4net.config.xml from assembly choco, Version=0.9.10.0, Culture=neutral, PublicKeyToken=79d02ea9cad655eb
2015-10-08 08:47:56,795 [DEBUG] - Configured chocolatey.infrastructure.logging.log4net.config.xml from assembly choco, Version=0.9.10.0, Culture=neutral, PublicKeyToken=79d02ea9cad655eb
2015-10-08 08:47:56,826 [DEBUG] - XmlConfiguration is now operational
2015-10-08 08:47:57,154 [DEBUG] - Attempting to delete file "C:\ProgramData\chocolatey\config\chocolatey.config.update".
2015-10-08 08:47:57,217 [INFO ] - 0.9.10-beta1
2015-10-08 08:48:08,873 [DEBUG] - Configured chocolatey.infrastructure.logging.log4net.config.xml from assembly choco, Version=0.9.10.0, Culture=neutral, PublicKeyToken=79d02ea9cad655eb
2015-10-08 08:48:08,873 [DEBUG] - Configured chocolatey.infrastructure.logging.log4net.config.xml from assembly choco, Version=0.9.10.0, Culture=neutral, PublicKeyToken=79d02ea9cad655eb
2015-10-08 08:48:08,920 [DEBUG] - XmlConfiguration is now operational
2015-10-08 08:48:09,232 [DEBUG] - Attempting to copy "C:\ProgramData\chocolatey\config\chocolatey.config.update"
to "C:\ProgramData\chocolatey\config\chocolatey.config".
2015-10-08 08:48:09,248 [DEBUG] - Attempting to delete file "C:\ProgramData\chocolatey\config\chocolatey.config.update".
2015-10-08 08:48:09,310 [INFO ] - 0.9.10-beta1
2015-10-08 08:48:10,185 [DEBUG] - Configured chocolatey.infrastructure.logging.log4net.config.xml from assembly choco, Version=0.9.10.0, Culture=neutral, PublicKeyToken=79d02ea9cad655eb
2015-10-08 08:48:10,185 [DEBUG] - Configured chocolatey.infrastructure.logging.log4net.config.xml from assembly choco, Version=0.9.10.0, Culture=neutral, PublicKeyToken=79d02ea9cad655eb
2015-10-08 08:48:10,217 [DEBUG] - XmlConfiguration is now operational
2015-10-08 08:48:10,560 [DEBUG] - Attempting to delete file "C:\ProgramData\chocolatey\config\chocolatey.config.update".
2015-10-08 08:48:10,639 [DEBUG] - Chocolatey is running on Windows v 6.3.9600.0
2015-10-08 08:48:10,639 [DEBUG] - Attempting to delete file "C:/ProgramData/chocolatey/choco.exe.old".
2015-10-08 08:48:10,639 [DEBUG] - Attempting to delete file "C:\ProgramData\chocolatey\choco.exe.old".
2015-10-08 08:48:10,654 [DEBUG] - Command line: "C:\ProgramData\chocolatey\choco.exe" list -lo -r
2015-10-08 08:48:10,654 [DEBUG] - Received arguments: list -lo -r
2015-10-08 08:48:10,732 [DEBUG] - The source 'https://__OUR__LOCAL__REPO__/chocolatey;
https://chocolatey.org/api/v2/' evaluated to a 'normal' source type
2015-10-08 08:48:10,732 [DEBUG] -
NOTE: Hiding sensitive configuration data! Please double and triple
check to be sure no sensitive data is shown, especially if copying
output to a gist for review.
2015-10-08 08:48:10,748 [DEBUG] - Configuration: CommandName='list'|
CacheLocation='C:\Users\ADM_FR~1\AppData\Local\Temp'|
ContainsLegacyPackageInstalls='True'|
CommandExecutionTimeoutSeconds='2700'|
Sources='https://__OUR__LOCAL__REPO__/chocolatey;
https://chocolatey.org/api/v2/'|SourceType='normal'|Debug='False'|Verbose='False'|Force='False'|
Noop='False'|HelpRequested='False'|RegularOutput='False'|
QuietOutput='False'|PromptForConfirmation='True'|AcceptLicense='False'|
AllowUnofficialBuild='False'|AllVersions='False'|
SkipPackageInstallProvider='False'|Prerelease='False'|ForceX86='False'|
OverrideArguments='False'|NotSilent='False'|IgnoreDependencies='False'|
AllowMultipleVersions='False'|AllowDowngrade='False'|
ForceDependencies='False'|Information.PlatformType='Windows'|
Information.PlatformVersion='6.3.9600.0'|
Information.PlatformName='Windows Server 2012 R2'|
Information.ChocolateyVersion='0.9.10.0'|
Information.ChocolateyProductVersion='0.9.10-beta1'|
Information.FullName='choco, Version=0.9.10.0, Culture=neutral, PublicKeyToken=79d02ea9cad655eb'|
Information.Is64Bit='True'|Information.IsInteractive='True'|
Information.IsUserAdministrator='True'|
Information.IsProcessElevated='True'|Features.AutoUninstaller='True'|
Features.CheckSumFiles='True'|Features.FailOnAutoUninstaller='False'|
ListCommand.LocalOnly='True'|
ListCommand.IncludeRegistryPrograms='False'|ListCommand.PageSize='25'|
UpgradeCommand.FailOnUnfound='False'|
UpgradeCommand.FailOnNotInstalled='False'|
UpgradeCommand.NotifyOnlyAvailableUpgrades='False'|
NewCommand.AutomaticPackage='False'|SourceCommand.Command='unknown'|
SourceCommand.Priority='0'|FeatureCommand.Command='unknown'|
ConfigCommand.Command='unknown'|PushCommand.TimeoutInSeconds='0'|
PinCommand.Command='unknown'|
2015-10-08 08:48:10,748 [DEBUG] - _ Chocolatey:ChocolateyListCommand - Normal Run Mode _
2015-10-08 08:48:11,092 [INFO ] - chocolatey|0.9.10-beta-20151007
2015-10-08 08:48:11,107 [INFO ] - git|2.5.3
2015-10-08 08:48:11,107 [INFO ] - git.install|2.5.3
2015-10-08 08:48:11,107 [INFO ] - notepadplusplus.install|6.8.3
2015-10-08 08:48:11,107 [INFO ] - nscp|0.4.3.143
2015-10-08 08:48:11,107 [INFO ] - puppet|3.8.3
2015-10-08 08:48:11,107 [INFO ] - splunk-universal-forwarder|6.1.1.207789
2015-10-08 08:48:11,107 [INFO ] - warmup|0.6.5.1
2015-10-08 08:48:11,107 [INFO ] - wintail|1.17.2
2015-10-08 08:48:11,107 [DEBUG] - Exiting with 0
2015-10-08 08:48:11,654 [DEBUG] - Configured chocolatey.infrastructure.logging.log4net.config.xml from assembly choco, Version=0.9.10.0, Culture=neutral, PublicKeyToken=79d02ea9cad655eb
2015-10-08 08:48:11,654 [DEBUG] - Configured chocolatey.infrastructure.logging.log4net.config.xml from assembly choco, Version=0.9.10.0, Culture=neutral, PublicKeyToken=79d02ea9cad655eb
2015-10-08 08:48:11,701 [DEBUG] - XmlConfiguration is now operational
2015-10-08 08:48:12,264 [DEBUG] - Attempting to delete file "C:\ProgramData\chocolatey\config\chocolatey.config.update".
2015-10-08 08:48:12,326 [DEBUG] - Chocolatey is running on Windows v 6.3.9600.0
2015-10-08 08:48:12,342 [DEBUG] - Attempting to delete file "C:/ProgramData/chocolatey/choco.exe.old".
2015-10-08 08:48:12,342 [DEBUG] - Attempting to delete file "C:\ProgramData\chocolatey\choco.exe.old".
2015-10-08 08:48:12,342 [DEBUG] - Command line: "C:\ProgramData\chocolatey\choco.exe" upgrade --noop nscp -r
2015-10-08 08:48:12,342 [DEBUG] - Received arguments: upgrade --noop nscp -r
2015-10-08 08:48:12,420 [DEBUG] - The source 'https://__OUR__LOCAL__REPO__/chocolatey;
https://chocolatey.org/api/v2/' evaluated to a 'normal' source type
2015-10-08 08:48:12,420 [DEBUG] -
NOTE: Hiding sensitive configuration data! Please double and triple
check to be sure no sensitive data is shown, especially if copying
output to a gist for review.
2015-10-08 08:48:12,451 [DEBUG] - Configuration: CommandName='upgrade'|
CacheLocation='C:\Users\ADM_FR~1\AppData\Local\Temp'|
ContainsLegacyPackageInstalls='True'|
CommandExecutionTimeoutSeconds='2700'|
Sources='https://__OUR__LOCAL__REPO__/chocolatey;
https://chocolatey.org/api/v2/'|SourceType='normal'|Debug='False'|Verbose='False'|Force='False'|
Noop='True'|HelpRequested='False'|RegularOutput='False'|
QuietOutput='False'|PromptForConfirmation='True'|AcceptLicense='False'|
AllowUnofficialBuild='False'|Input='nscp'|AllVersions='False'|
SkipPackageInstallProvider='False'|PackageNames='nscp'|
Prerelease='False'|ForceX86='False'|OverrideArguments='False'|
NotSilent='False'|IgnoreDependencies='False'|
AllowMultipleVersions='False'|AllowDowngrade='False'|
ForceDependencies='False'|Information.PlatformType='Windows'|
Information.PlatformVersion='6.3.9600.0'|
Information.PlatformName='Windows Server 2012 R2'|
Information.ChocolateyVersion='0.9.10.0'|
Information.ChocolateyProductVersion='0.9.10-beta1'|
Information.FullName='choco, Version=0.9.10.0, Culture=neutral, PublicKeyToken=79d02ea9cad655eb'|
Information.Is64Bit='True'|Information.IsInteractive='True'|
Information.IsUserAdministrator='True'|
Information.IsProcessElevated='True'|Features.AutoUninstaller='True'|
Features.CheckSumFiles='True'|Features.FailOnAutoUninstaller='False'|
ListCommand.LocalOnly='False'|
ListCommand.IncludeRegistryPrograms='False'|ListCommand.PageSize='25'|
UpgradeCommand.FailOnUnfound='False'|
UpgradeCommand.FailOnNotInstalled='False'|
UpgradeCommand.NotifyOnlyAvailableUpgrades='False'|
NewCommand.AutomaticPackage='False'|SourceCommand.Command='unknown'|
SourceCommand.Priority='0'|FeatureCommand.Command='unknown'|
ConfigCommand.Command='unknown'|PushCommand.TimeoutInSeconds='0'|
PinCommand.Command='unknown'|
2015-10-08 08:48:31,279 [INFO ] - nscp|0.4.3.143|0.4.3.143|false
2015-10-08 08:48:31,295 [DEBUG] - Exiting with 0
2015-10-08 08:48:31,998 [DEBUG] - Configured chocolatey.infrastructure.logging.log4net.config.xml from assembly choco, Version=0.9.10.0, Culture=neutral, PublicKeyToken=79d02ea9cad655eb
2015-10-08 08:48:31,998 [DEBUG] - Configured chocolatey.infrastructure.logging.log4net.config.xml from assembly choco, Version=0.9.10.0, Culture=neutral, PublicKeyToken=79d02ea9cad655eb
2015-10-08 08:48:32,045 [DEBUG] - XmlConfiguration is now operational
2015-10-08 08:48:32,451 [DEBUG] - Attempting to delete file "C:\ProgramData\chocolatey\config\chocolatey.config.update".
2015-10-08 08:48:32,654 [DEBUG] - Chocolatey is running on Windows v 6.3.9600.0
2015-10-08 08:48:32,654 [DEBUG] - Attempting to delete file "C:/ProgramData/chocolatey/choco.exe.old".
2015-10-08 08:48:32,654 [DEBUG] - Attempting to delete file "C:\ProgramData\chocolatey\choco.exe.old".
2015-10-08 08:48:32,670 [DEBUG] - Command line: "C:\ProgramData\chocolatey\choco.exe" feature list -r
2015-10-08 08:48:32,686 [DEBUG] - Received arguments: feature list -r
2015-10-08 08:48:32,889 [DEBUG] - The source '' evaluated to a 'normal' source type
2015-10-08 08:48:32,889 [DEBUG] -
NOTE: Hiding sensitive configuration data! Please double and triple
check to be sure no sensitive data is shown, especially if copying
output to a gist for review.
2015-10-08 08:48:32,920 [DEBUG] - Configuration: CommandName='feature'|
CacheLocation='C:\Users\ADM_FR~1\AppData\Local\Temp'|
ContainsLegacyPackageInstalls='True'|
CommandExecutionTimeoutSeconds='2700'|SourceType='normal'|
Debug='False'|
Verbose='False'|Force='False'|Noop='False'|HelpRequested='False'|
RegularOutput='False'|QuietOutput='False'|PromptForConfirmation='True'|
AcceptLicense='False'|AllowUnofficialBuild='False'|Input='list'|
AllVersions='False'|SkipPackageInstallProvider='False'|
Prerelease='False'|ForceX86='False'|OverrideArguments='False'|
NotSilent='False'|IgnoreDependencies='False'|
AllowMultipleVersions='False'|AllowDowngrade='False'|
ForceDependencies='False'|Information.PlatformType='Windows'|
Information.PlatformVersion='6.3.9600.0'|
Information.PlatformName='Windows Server 2012 R2'|
Information.ChocolateyVersion='0.9.10.0'|
Information.ChocolateyProductVersion='0.9.10-beta1'|
Information.FullName='choco, Version=0.9.10.0, Culture=neutral, PublicKeyToken=79d02ea9cad655eb'|
Information.Is64Bit='True'|Information.IsInteractive='True'|
Information.IsUserAdministrator='True'|
Information.IsProcessElevated='True'|Features.AutoUninstaller='True'|
Features.CheckSumFiles='True'|Features.FailOnAutoUninstaller='False'|
ListCommand.LocalOnly='False'|
ListCommand.IncludeRegistryPrograms='False'|ListCommand.PageSize='25'|
UpgradeCommand.FailOnUnfound='False'|
UpgradeCommand.FailOnNotInstalled='False'|
UpgradeCommand.NotifyOnlyAvailableUpgrades='False'|
NewCommand.AutomaticPackage='False'|SourceCommand.Command='unknown'|
SourceCommand.Priority='0'|FeatureCommand.Command='list'|
ConfigCommand.Command='unknown'|PushCommand.TimeoutInSeconds='0'|
PinCommand.Command='unknown'|
2015-10-08 08:48:32,936 [DEBUG] - _ Chocolatey:ChocolateyFeatureCommand - Normal Run Mode _
2015-10-08 08:48:32,951 [INFO ] - checksumFiles - [Enabled] | Checksum files when pulled in from internet (based on package).
2015-10-08 08:48:32,951 [INFO ] - autoUninstaller - [Enabled] | Uninstall from programs and features without requiring an explicit uninstall script.
2015-10-08 08:48:32,951 [INFO ] - allowGlobalConfirmation - [Disabled] | Prompt for confirmation in scripts or bypass.
2015-10-08 08:48:32,951 [INFO ] - failOnAutoUninstaller - [Disabled] | Fail if automatic uninstaller fails.
2015-10-08 08:48:32,951 [DEBUG] - Exiting with 0
2015-10-08 08:48:33,842 [DEBUG] - Configured chocolatey.infrastructure.logging.log4net.config.xml from assembly choco, Version=0.9.10.0, Culture=neutral, PublicKeyToken=79d02ea9cad655eb
2015-10-08 08:48:33,842 [DEBUG] - Configured chocolatey.infrastructure.logging.log4net.config.xml from assembly choco, Version=0.9.10.0, Culture=neutral, PublicKeyToken=79d02ea9cad655eb
2015-10-08 08:48:33,889 [DEBUG] - XmlConfiguration is now operational
2015-10-08 08:48:34,186 [DEBUG] - Attempting to delete file "C:\ProgramData\chocolatey\config\chocolatey.config.update".
2015-10-08 08:48:34,248 [DEBUG] - Chocolatey is running on Windows v 6.3.9600.0
2015-10-08 08:48:34,248 [DEBUG] - Attempting to delete file "C:/ProgramData/chocolatey/choco.exe.old".
2015-10-08 08:48:34,248 [DEBUG] - Attempting to delete file "C:\ProgramData\chocolatey\choco.exe.old".
2015-10-08 08:48:34,264 [DEBUG] - Command line: "C:\ProgramData\chocolatey\choco.exe" feature -r enable -n autoUninstaller
2015-10-08 08:48:34,264 [DEBUG] - Received arguments: feature -r enable -n autoUninstaller
2015-10-08 08:48:34,342 [DEBUG] - The source '' evaluated to a 'normal' source type
2015-10-08 08:48:34,357 [DEBUG] -
NOTE: Hiding sensitive configuration data! Please double and triple
check to be sure no sensitive data is shown, especially if copying
output to a gist for review.
2015-10-08 08:48:34,373 [DEBUG] - Configuration: CommandName='feature'|
CacheLocation='C:\Users\ADM_FR~1\AppData\Local\Temp'|
ContainsLegacyPackageInstalls='True'|
CommandExecutionTimeoutSeconds='2700'|SourceType='normal'|
Debug='False'|
Verbose='False'|Force='False'|Noop='False'|HelpRequested='False'|
RegularOutput='False'|QuietOutput='False'|PromptForConfirmation='True'|
AcceptLicense='False'|AllowUnofficialBuild='False'|Input='enable'|
AllVersions='False'|SkipPackageInstallProvider='False'|
Prerelease='False'|ForceX86='False'|OverrideArguments='False'|
NotSilent='False'|IgnoreDependencies='False'|
AllowMultipleVersions='False'|AllowDowngrade='False'|
ForceDependencies='False'|Information.PlatformType='Windows'|
Information.PlatformVersion='6.3.9600.0'|
Information.PlatformName='Windows Server 2012 R2'|
Information.ChocolateyVersion='0.9.10.0'|
Information.ChocolateyProductVersion='0.9.10-beta1'|
Information.FullName='choco, Version=0.9.10.0, Culture=neutral, PublicKeyToken=79d02ea9cad655eb'|
Information.Is64Bit='True'|Information.IsInteractive='True'|
Information.IsUserAdministrator='True'|
Information.IsProcessElevated='True'|Features.AutoUninstaller='True'|
Features.CheckSumFiles='True'|Features.FailOnAutoUninstaller='False'|
ListCommand.LocalOnly='False'|
ListCommand.IncludeRegistryPrograms='False'|ListCommand.PageSize='25'|
UpgradeCommand.FailOnUnfound='False'|
UpgradeCommand.FailOnNotInstalled='False'|
UpgradeCommand.NotifyOnlyAvailableUpgrades='False'|
NewCommand.AutomaticPackage='False'|SourceCommand.Command='unknown'|
SourceCommand.Priority='0'|FeatureCommand.Name='autoUninstaller'|
FeatureCommand.Command='enable'|ConfigCommand.Command='unknown'|
PushCommand.TimeoutInSeconds='0'|PinCommand.Command='unknown'|
2015-10-08 08:48:34,373 [DEBUG] - _ Chocolatey:ChocolateyFeatureCommand - Normal Run Mode _
2015-10-08 08:48:34,404 [INFO ] - autoUninstaller was enabled by default. Explicitly setting value.
2015-10-08 08:48:34,420 [DEBUG] - Attempting to copy "C:\ProgramData\chocolatey\config\chocolatey.config.update"
to "C:\ProgramData\chocolatey\config\chocolatey.config".
2015-10-08 08:48:34,420 [DEBUG] - Attempting to delete file "C:\ProgramData\chocolatey\config\chocolatey.config.update".
2015-10-08 08:48:34,420 [WARN ] - Enabled autoUninstaller
2015-10-08 08:48:34,420 [DEBUG] - Exiting with 0