Couple of things:
What version of package Builder? Are you using 8.8?
Is the applicaiton rebooting the system? If yest try not letting the app reboot (if possible) and reboot yourself.
What client OS/SP?
I've seen this with older versions of PB. Also, I would only use a snapshot as a last resort. Too many negatives. There are very packages that you will need to do a snaphot.
After the machine has rebooted open the package builder wizard again, click on scan options, select Reuse existing scan, click Ok, click next. The wizard should then allow you to do the comparison scan.
The best way is following the Vendor’s Specifications for choosing package type. Most applications already include a method for an unattended installation making a packaging tool unnecessary. Packaging utilities should only be used when there are no vendor installation parameters. You may take a look at this Community document:
Best Known Methods for Software Distribution
In the attached .pdf file see page 7.
To find some installation hints (switches, parameters, instructions), try a look here:
Thanks everyone for the ideas, suggestions, etc...