This would probably go better in the workbench section... But i'll help you.
I think what you have to do, off the top of my head as a guess, is go to the swkotor2.ini and change the option under display options, change FullScreen=1 to FullScreen=0.
If it doesn't work then I'll see if I can figure out some way else to do it.
Please feed the trolls. XD