When I am deploying a NEW Virtual Software Package, and I have it where I like it there are a few steps I do to "CLEAN-IT-UP" and prepare it for Distribution as a .VSA file through Altiris.
First thing I do is RESET the layer.
Second thing I do is go to the c:\FSLDR\# and delete the folder that looks like this S-1-5-21-112987585-3770-..... As far as I can tell, that is a SID and can not be in a Clean package.
Third thing I do is go to REGEDIT
HKLM\Software\FSLDR\2\HU\S-1-5-21-112987585-3770-..... Then I delete this one too.
At this point the layer is as clean as it can be....and I have found it to be SAFE to export. Export to a TEST machine and give it a shot.
Good Luck to everyone.
Thanks - Tom Fronza