I downloaded the code from sourceforge and replaced my version to test and at first it hung, like it did for you. I think this is because it wasn't installed by the installer. Here is how I got around the issue:
1. Open cmd prompt
2. Copy entire updatePaths.pl commandline generated by Petunia updatePaths page to the command line and run it. Windows should ask you for permission to run perl interpreter on this file, allow it!
3. updatePaths.pl should now run to completion and you should be able to use Petunia to run it also
This worked for me, let me know if it does or doesn't work for you.