I am almost as far to publish the version 0.3.0.0.
Unfortunately, i had no time to continue to care about your problem.
You can try to delete (better rename to .bak) the file "settings.ini" in the folder that contains the file "xcomextractor.exe". That effects that you must set your paths again. Maybe that helps, but i do not think so, but its a try.
Can you post me the line of your settings.ini here, that starts with "PFAD BB-Toolkit: "