OK, have you tried using Windows 2000's Disk Manager to see what it's reporting? For example, it may be possible that it's only seeing a certain amount of partitioned/formatted space, but maybe more is showing up as unallocated...
Start/Administrative Tools folder and select Computer Management, Storage, Disk Management...
Seems like you're savvy about a lot of this stuff, so hope you're not offended by the suggestions...just trying to think of everything.