You're comparing apples and oranges without more info.
I suspect that it's a lack of RAM issue, but that's my bias.
Try hitting C-A-D and bringing up the Task Manager then looking at the Performance tab. Look at the memory totals.
On this Win2K machine I've got 35 processes; 111,820 kB total committed; 512 MB total physical with 409,832 kB available, 34,892 kB total kernel memory with 8.2 MB non-paged. Athlon XP 1900+ (1.6 GHz). Win2k quite snappy (but I haven't tried Win9x on it to make a comparison).
The boot partition is NTFS and the other partitions are all FAT32.
HTH.
Cheers,
Scott.