I have 2 500gb Comstar external hard drives running on my Windows 2000 system (Labeled H: and I .This has been working for months but today I rebooted and windows only saw one drive. After a few reboots and swapping ports etc I came to the conclusion that the PC can see either H: or I: but not both at once any more. When I plug the 2nd drive in, windows will pop up a message that it wants to reboot, but rebooting doesn't fix it.
Both of these drives are working, because I tested them on another system.
It's possible that your system can't provide enough power for both hard disks to run at the same time. Though external hard disks require minimal power. In any case, did you add a new component to your computer?
Also, have you downloaded the latest for your motherboard and chipset?