Did you try manually setting the FPS limit to 50? That seems to be where my PC wants it hanging. It might be 60 if you're using an NTSC BIOS; mine is from my PAL PS2. also, you may have flipped the toggle from automatic frame-limiting to manual and set it too high or even accidentally set it to frameskip.
Also, ulaoulao was skitting you about how you seem to only have noticed it being too fast after 5 hours.