the control panel idea is probably a good one. go to it, and it should have the slide bar for 3d applications. you might have it set to "nice," which adds modifications by default. if so, slide it to "let the 3d application decide".
I made it work!!!! Found me a 30 fps ini file and that made the game run at normal speed it disabled my bosses mod but atleast i can play with other mods now and engoy the extra depth of nvidia 3d vision, pops out a bit more than the ps3 version!!