ISBoxer only forces windowed it if there's multiple characters in the Character Set. So no, if you only run the 1 on the 1 PC, with the current build of ISBoxer, it does not force it into windowed mode (even if you link another Character Set to it for multiple PC use). There's no other criteria, you can't change any other settings (borders etc) to change the behavior.

As I said, though, I can make a change for you