Long time ago, I struggled with sort of the same problem and I reckoned it had something to do with the SATA drivers installed.
I followed the following steps ( originally for XP, but worked fine in W2K) :
While loading Win 2000 on a computer with a serial ATA (SATA) hard drive, you will have to manually load the SATA drivers.
Copy the drivers from motherboard support CD *\DriverDisk\SATA\*.* into root directory of floppy disk. (i.e. root directory of floppy disk should contain \pide and \sata folders, txtsetup.oem, etc. files.)
Then, boot system by Win 2000 installation CD, when the message "Press F6 if you need to install a third party SCSI or RAID driver" shows up, press "F6". Then, press "S" to specify additional device when next screen pops up. Put the driver floppy disk you made in and press enter to continue. If the floppy disk is made successfully, the installation program will ask for selecting driver. Please then select "VIA Serial ATA RAID Controller(Win2000)".) After SATA driver loaded and Win2K can recognize the SATA HDD, you can continue to install Win2000 . The added HD should now give you 300Gb.
Hth