Sorry, I missread that you had gotten to Win2K. The problem might not in the MB bios. The only thing I might verify in the Bios is a setting which allows Plug and Play to be active. Win2K is plug and play, and it should detect new or different hardware. Since the hard drive controller is part of the motherboard, going to the new board will be going to a new controller. Win2k should redetect it, although why it isn't, I'm not sure.
If it is the controller and Win2k can't automatically adjust, you'll have to change it manually. Try this first, although it may not be possible. Start Win2K in safe mode to remove and reinstall (redetect) the hard drive controller. If it doesn't work, see if you can start from the CD, and fix it through there.
If you can't get it restored, (and I'm not sure I'm suggesting everything), one really complicated solution might be to hook up things to your old motherboard, get in to Win2K, go into the device manager and remove the hard drive controller. Shut down the machine, attach your new motherboard and hopefully it will detect the new controller correctly.
On a side note, I did see this error crop up in Win2k on my own system, and it was caused by a malfunctioning SCSI hard drive controller. Are there any other storage devices on your system that might have skewed drivers (hard drives, CD-ROM/RW drives, Zip/Jaz drives, etc). It wouldn't hurt disconnecting those just to see if the problem goes away... If it does, you'll have to reinstall the appropriate drivers for that device.