I am trying to trial you Package aware to re-package some old applications, I can run the 'Before' and 'After' Scan and it creates all the files and tells me I can use InstallAware to package it.
When I open the package created by PackageAware in InstallAware it just crashes and gives a 'Not Responding' Error in Task manager. I left it for 30mins to make sure its not super-slow loading (which I doubted as its an ample spec PC)
If you are repackaging very large setups (they can install a very large amount of files, and/or create a very large amount of registry keys), this can occur. What is the setup you are trying to capture?