On the LMM GM now have much smarting programming history tracking. On the 05's this was not the situation, whilst they can see all the part numbers and CVN for each segment with a TechII they can't see what was in it in the past, only what is installed now.
On your Kodiak, if you read the stock tune and modified it from there then your Part numbers will match but the CVN's will be wrong, GM check the CVN's to those listed on the CalID website. If the tune is put back to stock then the CVN's will match, only the LMM keeps a history of previously programmed part numbers/CVN's.
It is possible that depending where you got your Kodiak from (ie coach builder) that the CVN's were never "stock" to begin with.
Cheers,
Ross (using Cindy's login)