You can boot to a DOS boot disk. That's good. Can you then change the disk and do a DIR and see the new disk? (This verifies the change line.)
At this point, you have two installs of the operating system saying that it can't communicate with the A drive. I'd try replacing the drive, even though the machine can boot from it.
If a new drive gives the same problem, then it looks like you might have a motherboard issue. Chat with the hardware vendor about the issue.
If the vendor says, "Hey, mate, the blinkin' drive works in the sweet land of DOS so life is good for me" then you might want to try flashing the BIOS to the most current version of the firmware. This isn't likely to be the problem because the drive worked for a while in W2k, but it's worth a shot. This could be an ACPI issue.
You might also want to try installing W98 to see if you get the same symptoms. If it works in W98, that would also tend to implicate ACPI on the machine.