Another note to add to this issue, I think I'm getting closer to figuring out some of the lower level issues here. CCP is building multiple packages for us (both when we build a single package or when we build one-off packages per product) that are using the same mediaSignature.
Just guessing but I think this is probably the root of all of the issues we're having here. When using Munki it certainly is, after some digging in the source it seems like Munki is using the mediaSignature as a sort of unique identifier. Not sure if this is related to the failed manual installations yet ...
Just talking to myself here ... carry on folks