It sounds like SWTOR is not set to be running in Windowed mode inside the game. I saw that same problem when I had the game set to fullscreen(windowed). You may need to change it manually in the ini file(s). They are in C:\Users\[User]\AppData\Local\SWTOR\swtor\settings and are named client_settings-xxxxxxxx.ini where the x's are you character name from ISBoxer. In those files you need to set d3dfullscreen=false instead of true.

As always, back up your files first.
Alge