Thanks for the quick responses! I can confirm the files are there and I have been running the prepare phase with verbose logging, this is the detail it gives at the point of the exception:
...
2018-03-20T12:05:30.0686834Z sonar.host.url={local 7 sonarqube server address}
2018-03-20T12:05:30.0686834Z sonar.projectKey={projectKey}
2018-03-20T12:05:30.0686834Z sonar.projectName={projectName}
2018-03-20T12:05:30.0686834Z sonar.projectVersion=1.0
2018-03-20T12:05:30.0686834Z sonar.verbose=true
2018-03-20T12:05:30.0686834Z sonar.visualstudio.enable=false
2018-03-20T12:05:30.0686834Z
2018-03-20T12:05:30.0686834Z sonar.modules=DA7EC545-D974-45EB-9758-B917C4BAB3E3,5AE5BA00-FBF9-4802-95DA-567AE5A448DF,A48F7B15-E52B-4820-8C8F-170C523DA625,32347D63-9DA5-4CED-AD68-E1F2A7D83EE6,7D4CFC24-28E1-479F-BE36-B61D64FA8E47,0A507097-2506-4FF1-8963-FC188B80B439,994DC638-18A8-48D1-ACE0-B244BB0FBFC8,7A904C84-EFB1-41A6-82B9-D68A845CBBAD,07BF9B2F-25B8-4C9A-BA6B-440BFDC7D5ED,0B713C0B-3E99-4B7C-A9D6-5B31594BBF5A,34865112-F47B-498E-BE7B-7411364D0238,A13E3A3D-FB02-480D-A7B5-99C3F78CB318,EDE2C9D0-8385-4CBD-B602-53037D8AB763,E1ADAAE1-1337-4C81-A662-48C030938E0B,A7DE21A6-8822-4613-959D-5CD7C2DF4466
2018-03-20T12:05:30.0686834Z
2018-03-20T12:05:30.0686834Z
2018-03-20T12:05:30.0686834Z ------------------------------------------------------------------------
2018-03-20T12:05:30.0686834Z Writing processing summary to C:\agent1\_work\11\.sonarqube\out\ProjectInfo.log
2018-03-20T12:05:30.0686834Z SONAR_SCANNER_OPTS is not configured. Setting it to the default value of -Xmx1024m
2018-03-20T12:05:30.0686834Z Calling the SonarQube Scanner...
2018-03-20T12:05:30.0686834Z Setting environment variable 'SONAR_SCANNER_OPTS'. Value: -Xmx1024m
2018-03-20T12:05:30.5687332Z
2018-03-20T12:05:30.5845773Z Unhandled Exception: System.ComponentModel.Win32Exception: Access is denied
2018-03-20T12:05:30.5845773Z at System.Diagnostics.Process.StartWithCreateProcess(ProcessStartInfo startInfo)
2018-03-20T12:05:30.5845773Z at SonarScanner.MSBuild.Common.ProcessRunner.Execute(ProcessRunnerArguments runnerArgs)
2018-03-20T12:05:30.5845773Z at SonarScanner.MSBuild.Shim.SonarScannerWrapper.ExecuteJavaRunner(AnalysisConfig config, IEnumerable`1 userCmdLineArguments, ILogger logger, String exeFileName, String propertiesFileName)
2018-03-20T12:05:30.5845773Z at SonarScanner.MSBuild.Shim.SonarScannerWrapper.InternalExecute(AnalysisConfig config, IEnumerable`1 userCmdLineArguments, ILogger logger, String fullPropertiesFilePath)
2018-03-20T12:05:30.5845773Z at SonarScanner.MSBuild.Shim.SonarScannerWrapper.<>c__DisplayClass6_0.<Execute>b__0()
2018-03-20T12:05:30.5845773Z at SonarScanner.MSBuild.Shim.SonarScannerWrapper.Execute(AnalysisConfig config, IEnumerable`1 userCmdLineArguments, ILogger logger)
2018-03-20T12:05:30.5845773Z at SonarScanner.MSBuild.PostProcessor.MSBuildPostProcessor.InvokeSonarScanner(IAnalysisPropertyProvider cmdLineArgs, AnalysisConfig config)
2018-03-20T12:05:30.5845773Z at SonarScanner.MSBuild.PostProcessor.MSBuildPostProcessor.Execute(String[] args, AnalysisConfig config, ITeamBuildSettings settings)
2018-03-20T12:05:30.5845773Z at SonarScanner.MSBuild.BootstrapperClass.PostProcess()
2018-03-20T12:05:30.5845773Z at SonarScanner.MSBuild.BootstrapperClass.Execute()
2018-03-20T12:05:30.5845773Z at SonarScanner.MSBuild.Program.Execute(String[] args, ILogger logger)
2018-03-20T12:05:30.5845773Z at SonarScanner.MSBuild.Program.Main(String[] args)
2018-03-20T12:05:30.6155803Z ##[error]C:\agent1\_work\_tasks\SonarQubePrepare_15b84ca1-b62f-4a2a-a403-89b77a063157\4.1.0\classic-sonar-scanner-msbuild\SonarScanner.MSBuild.exe failed with return code: 3762504530
2018-03-20T12:05:30.6312056Z ##[section]Finishing: Run Code Analysis
I can also confirm that the build agent services is logging on and running as the user we've configured to be a member of the local administrators group.