Whenever I'm using a program that is DirectX or something that runs in a window or full-screen, I seem to have some problems switching to it, and litestep keeps minimizing and breaking it. Also, it won't let the mouse be used inside the program? Just as an example I'll use Zsnes... the mouse will not work inside the program!
Is this a problem... or am I missing something?

does your theme use jdesk?