To me it sounds like your CMOS battery might be flat, this would cause the PC to behave strangely and for it to say that the
CPU settings have been changed.
Have you noticed the time/date in windows being wrong.
If you have a multi-meter at home (which most people don't) you could test the battery and make sure it is at the recommended 3.3 volts.
Otherwise as you say it could have something to do with the motherboard, but check out the CMOS battery first. If you don't have a multimeter then just buy a new battery (they are cheap) and replace it. When you first replace it, it will tell you that your
CPU settings have changed again and you will possibly need to change your date and time.