Do you do any "cleanup" of the application object before pushing it out to the workstation? If you can go back to the original aot/axt file after the original snapshot, do they show up then?
It sounds like a registry key was deleted that should not have been. You may want to look into Centralis Axe for automating the "cleanup" of a nal. It automatically will get rid of un-necessary reg keys, files, etc.