Your settings should stay intact with an upgrade. Also, GameEx backs up your settings in case. You could also backup your settings as a safety measure. As far as your issue, the way I would approach this is by troubleshooting with the runitgame.bat file. Instructions on how to do so are on the pinned "How To Ask For Help" topic found on the top of the forums. Follow step 4B on how to do this. This will show the command-line window and will show exactly what's being displayed on the screen and should provide useful info on why it's being returned back to GameEx.