I've always had my drives formatted NTFS, but I was wondering can you still stripe your hard drives, etc. in Win2K if you use the FAT32 file system? Also, isn't there a drive size limitation with FAT32? I may be way off base here....just wanted to refresh my memory.
Jerry- I say go with NTFS unless you're going to dual boot. I have a feeling that your problems with latency and skipping are probably OS related (ie 98 vs 2000) not FAT32 vs NTFS. Make sure you have the latest drivers, etc. for your card with 2000.