if you had bios problem you wouldn't be able to boot into windows at all.
I am not saying this is what is happening to you but I made a very stupid mistake recently when I builted a new computer. I keep getting a error massage about cpu fan temperature; it turned out I connect the thing in the wrong place (they were next to each other).
I am running Windows XP_sp2 on a Sony Vaio PCV-RS520 with an Intel P-IV, 3000MHz and 1.5GB memory. Early last year, after booting up, instead of Windows starting up I would get a screen detecting all my drives, etc., and at the bottom was a message noting "POWER FAN IS ABNORMAL! (F2) to Run Setup." I had the fan replaced but about a month later it did it again. This time the technician just went to the BIOS setup utility and clicked on "DEFAULT" and the message stopped. (When this happened the second time, I believe it was shortly after I had reformatted my hard drive.)
This past October, because of a bug in a program, I had to reformat my hard drive again. After doing so, I downloaded and installed all the updates from Sony that I had lost due to reformatting. However, I also downloaded a BIOS update. (I should mention here that I don't know if I had downloaded this BIOS update after reformatting the first time.)But, becuase I couldn't get it boot into Windows after clicking on "LOAD SETUP DEFAULTS" in the BIOS SETUP UTILITY, I called the company I have a service contract with who told me that it was caused by my (possibly) re-installing the BIOS update-that it wasn't necessary. But, several other people I have talked to about this tell me I probably wouldn't be able to boot into Windows at all, and/or would have many other types of problems.
I am hoping that someone can give me some idea as to whether I might have caused this and, if so, how I can correct it? Or, if I should just go get another fan installed and see if it goes away.