First of all, do you know how to get to the Gamedata/base folder? If you know, then I can help you!
Does the fullscreen problem happen on SP and/or MP?
Anyways... Depending on what the total problem is, click on Jaconfig or Jampconfig (Jamp is for MP and Ja is for SP) and find
Seta r_fullscreen "X"
(X stands for 1 or 0, 1 equals full screen and 0 means NOT full screen)
So find it, switch it to 0 and then POOF you're done!