I've seen lots of cases of Windows 2000 taking 5 minutes to boot. Sorry that the most common case isn't what you're expecting, but there is a reason to mention it. If your machine is ordinarily connected to a LAN, but if you disconnected it from the LAN in order to use it with GPIB and your instruments, then this might be your situation. If your LAN card is configured to get an IP address automatically as a DHCP client, then Windows 2000 will try about 5 times to contact a DHCP server during boot, and then give up after timing out about 5 times. To avoid this, assign a fixed IP address to your LAN card when you're disconnected (e.g. 192.168.200.200). Don't forget to change it back afterwards.
If the delay is really due to Windows corrupting itself due to detection of hardware changes, then I could try making a few guesses. Although PCI boards aren't "supposed" to have much trouble with assignment of resources, various combinations of motherboards and PCI boards and OSes do. Try moving the board to a different slot. Another thing to try is, with the board inserted, open up Windows Device Manager and use the menu commands to delete the device from there. Then shut down and power off, physically delete the device from the computer, and boot again. If you did the physical removal first then there is a trick to get device manager to display the device if there is still information in the registry about the device, in order to use the menu commands to delete Windows' memory of the device. But I don't recall the trick, sorry. Without it, the nonexistent device doesn't show up and can't get fully deleted. (I know this doesn't sound believable, but you have to remember that this is Windows we're talking about.)
After it's fully gone, do this cumbersome procedure to try installing again. Install the drivers, shut down and power off, install the board, boot, wait for Windows to figure out that the driver works for the board, shut down and power off again, boot again, and look to see if the driver is really working. By the way I have even had to do this with GPIB-USB-B, not only with PCI-GPIB. I have a sneaking suspicion that Microsoft is only 90% to blame in this particular case.
