If you're able to, check to see what you have starting up when Windows does. If you can use the 'Run' menu, type in "msconfig". If you're unsure of what's starting, just post a list. Could be a utility to check to make sure everything is okay w/ the system.
If you're not having any problems w/ the system besides that, it could be a "false positive". Could also be that your HDD is getting ready to go South.
If it has parts that you can get to, you could try booting w/ a mfr floppy to test the HDD. You can find a handy list
here Are you able to get into the BIOS? You should be able to identify the HDD that way.
If you don't have a floppy or a way to access the actual parts, then you'll probably have to live w/ it or get somebody who services them to check it for you.