At the risk of sounding like a broken record, how sure are you that you've checked all the BIOS settings? Usually the Basic CMOS Settings will have the floppy and hard drives. You might have to manually set it to Disabled if it somehow thinks you have one.
And on the Advanced or maybe Chipset page there's usually another one or two about Enabling Floppy drives and Boot-Up Floppy Seek.
Also, if there's a cable in the FDD channel on the MB, that could confuse it.
If it really isn't a BIOS issue, the only thing I could imagine is that there is another feature on your motherboard that Windows is confusing with a Floppy drive. In that case, you should make sure you have the latest drivers for your motherboard's chipset and controllers.