Hello,
I am curious if the computer's BIOS properly registers the second hard drive, and am curious if your computer was running something else, like a linux, before turning it into a Win 2000 box. Windows 2K would recognize FAT or FAT32 as a hard drive format, but perhaps if you ran linux on the box, it might be choking on ext2 or something.
It is also possible that the hard drive is suffering from a physical problem. I have yet to run into a normal IDE drive that W2K could not work with.
Consider though:
* Is the drive SCSI? If so, did you install the SCSI driver that the OS might need to work with it?
* Is the drive SATA (Serial ATA?) That is after W2K's time... might need the driver disk.
Does WIndows show you any devices out-of-whack in the Device Manager?
Christian