Yes, I know what the problem is. I searched high and low, posted on here, and nobody could help. Finally, I found an answer!
Let me guess, at one time or another you had win98 (or other OS) installed previously? I was messing around and was dual booting to 98.. etc etc. Then, instead of formatting, I just deleted win98 directory, and reinstalled 2k. Then I was getting that message.
It has to do with something in the boot record I believe. A trace of win98 or whatever. It poses no problems to you or windows currently, so don't worry about it. It is annoying I know, but I just reformated and I haven't noticed the error since. So, I think that's the only solution, but they may be another if anyone cares to help out and give me some more info.