Does it work for you if you just change the name of primary data container or shortcut executable in the package.ini and rebuild? For example,
From:
[App.exe]
......
ReadOnlyData=Package.ro.tvr
......
[ShortcutApp.exe]
Shortcut=App.exe
To:
[App1.exe]
......
ReadOnlyData=Package.ro.tvr
......
[ShortcutApp1.exe]
Shortcut=App1.exe
Then you will get App1.exe and ShortcutApp1.exe.
