I'm having a problem with the Config file.

When I launch the pack for the first time, it gets created, then I modify everything to my taste. But after launching the pack again, the Config files changes everything to a new format.

Original file with my changes:
http://pastebin.com/8RGNfDMP

New modified file after 2nd launch:
http://pastebin.com/qvD4Y9JD

PS: Even after tweaking the 2nd file, all the changes are ignored and reset to defaults.

I'll look into that. I've always changed my settings through the Mods menu (on title screen, click Mods > select WIT > click Config). Try that and let me know if the changes are saved.