I had a problem quite similar to yours... but it was with version 3.0 and I don't know if the bug was resolved in version 3.01.
Did you disable the welcome screen of IS Repackager? Then that might be the problem.
To re-enable the welcome screen, go to the Windows folder, open isrepackager.ini and set ShowWelcomePage = 1.
Hope this helps... 🙂