The nVidia nForce3 250 chipset on your new motherboard support SATA ports, while the nForce2 chipset on your old motherboard does not. This makes nForce3 more complicated to configure properly.
I don’t know the details of your nForce3 250 motherboard, but I would suggest going into the BIOS setup to look for a setting that controls the resource allocation of PATA/IDE and SATA ports. The exact description of such a setting can vary among motherboards, and can be a bit tricky to locate. In some cases, it may not even exist.
If you can find such a setting, I recommend setting the PATA/IDE ports to use legacy/compatible resources (IRQ 14 for primary IDE, IRQ 15 for secondary IDE, etc.), which implies the SATA ports will be configured to use native (non-legacy) resources. This configuration should have the highest degree of compatibility with various OS’es.
Another thing you can do is check whether the IDE channel (primary or secondary) the Plextor Premium is attached to is utilizing legacy resources. Go into the Win2000 device manager, and do “properties” on the primary or secondary channel (under the IDE ATA/ATAPI controllers section), and click on the “resource” tab. If you see IRQ 15 for secondary IDE or IRQ 14 for primary IDE, then the IDE channels are in legacy resource mode, which is the most compatible mode. If you don’t see IRQ 14 or 15 for IDE then go into BIOS setup to see if you can reconfigure as described above.
Also try updating to the latest PlexTools Professional 2.15 for the Plextor Premium. Your problem may be a case where PlexTools Pro needs a bit of “help” to work properly with the nForce3 250 chipset.