Hi. SWTOR may have reset you to full screen mode. You can probably hit Alt+Enter to toggle the game back into windowed mode. After toggling into windowed mode, it will probably look wrong still. To complete the process you can close the window, and re-launch your team. Alternatively, you might be able to use the Reload button from the in-game ISBoxer Control Panel (Ctrl+Shift+Alt+G) or an Export to Inner Space (through ISBoxer) at that point.

The current ISBoxer 40 Beta includes a check for this when you Export.