Bryan,
I ran into this problem when repackaging WinZip as well. The recommended solution from WinZip is as follows (from their web site) :-
"Silent (On Demand) Installs (AUTOINST.TXT)
In some network environments, WinZip may repeat the installation process (including the Setup Wizard) each time it is run from a workstation. This occurs when the network environment does not preserve WinZip's user registry settings between WinZip sessions.
If you encounter this situation, you can eliminate the repetitive installation process by creating a file called AUTOINST.TXT in each WinZip folder. This file, which must be a plain text file, must contain this exact text:
I agree to the WinZip Computing License Agreement
If this file is present and contains the specified text, WinZip will silently re-create the required registry information as needed each time it is run and your users will not see the Setup Wizard.
Note: if you are upgrading to WinZip 8.1 from a previous version of WinZip installed on a shared network drive, we suggest that you uninstall the previous version of WinZip (and delete any files left in the WinZip folder) before installing WinZip 8.1 and adding AUTOINST.TXT. Alternatively, you can simply look for the file WZSHLEXT.DLL in the WinZip folder. If it exists, delete the file. "
This solved the problem with WinZip for me. As for other apps, well I wish all the solutions to repackaging problems were as easy as this one.
Regards,
Dave