No my CPU is not overclocked. It's 3.0GHz stock. I've tried 3D 10 Hardware and 3D 9 Hardware, native turned on and off and a few other things. Changing my video plugin settings never seemed to do anything about the slowdown. I don't think I really changed any of the sound settings though, so I might try that. Like I've said I'm kind of apprehensive of doing anything else with PS2 emulation since I bluescreened.
Edit: Just tried those settings and I still get slowdown.