It sounds as if it will automatically disable parts of the cpu (cores), which would slow down your cpu overall. Kind of like how in the P4's with Hyper Threading, you can disable Hyper Threading in the BIOS, which slows down the computer a bit, but makes it so that it's compatible with some older programs that don't support Hyper Threading.
Try updating to the recent ones (2/12/01) and see if that helps. If not, then I'd reset the BIOS to what it was when you first got it (because you know it works!). You can do this by pulling the cmos battery for about a minute, then reinstalling it and rebooting. Some motherboards have jumper pins (near the cmos battery usually) that you need to move also. Refer to your motherboard manual to double check and see exactly how to reset the bios, it's quite simple and should tell you step by step what to do.
Let us know if this helps!
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