Shocker, I know, computer related technical difficulties. However I don't believe I have ever seen anything like this. I simply boot up Alpha Protocol and it runs fine. Except for the fact that all of the characters polygons are outlined and pop in and out of their skin. My secondary video card just recently blew up, and I will be getting that back soon and it will probably fix it. But in the meantime I was wondering if there were any video options I could toggle to fix the problem.

Try reinstalling your graphics driver perhaps? Sounds like something is all screwy with that.
 
Also listing you pc's specs would help figure this out too.