You should only see xml files in the generated cab files if the package happens to contain xml. One notable example would be packages in the third party catalogs that leverage packageboot. Additionally, the warning message posted is a bit truncated. Can you post in the full message?
I ended up just removing all Applicability and Installed rules since they always fail when trying to test for a file. I just push it out manually group by group. I always have to do a Update Agent Repair, then a Certificate push, then it installs ok. So far I'm having to do this with a BIOS settings package, a Adobe Reader 7u21 upgrade that removes all other versions, and the latest Adobe Reader 11.3.03.37 because Solarwinds didn't publish an Upgrade Only package for some reason.