This in not a munki specific problem. I have seen it happen when one tries to manually install an update. I don't have a solution except to install the update with a terminal command which always works.
Here is an example with an office update. It must be ran as an administrator.
installer -pkg "/path/to/Office 2011 14.2.3 Update.pkg" -target /
-----------------------------------------------------------------------
“Weaseling out of things is important to learn. It’s what
separates
us from the animals.....except the weasel” ~ Homer Simpson
I am having this same issue, but with Office 2008. So far I have determined that if the Office2008.dmg in the repo is manually mounted and the installer run, all subsequent Office2008_update items
install as expected down the line. If Office 2008 is installed by Munki, I'm stuck at 12.0.0. The 12.1.0 update throws that same error.
I'm taking a break from trying to figure this out. :/
:Dan