Okay so, I made the default windows transparency color set to one that i'd never use. Awsome, so anything that color is going to become see through. One problem, if I change anything to be that color (mainly because I want the output box's background transparent) then I can't move it or select it! Ahh the agony!
So I go back, and hope that I can create a new window and delete the old one. AH! No delete button! so I had to remake the interface file and a new interface.
Partially a bug maybe, partially a delete button request! and, maybe a 'transparent' check option should be available in each boxes appearance -> background/foreground section, request. ^^