It is possible that your mobo has a HD size limit. I think the limit on Windows XP's drive size is 4 Terrabytes, so it's not the OS.
There are a couple of things to consider when choosing a format for your HD: the first is compatibility. If you want to run any 16-bit programs (which is a feat for XP to accomplish in most cases) you'll want to run FAT32. However, if you are only running 32 or 64 bit applications, want added stability, or need added security or encryption you should try NTFS.
The other consideration is speed. For drives that are 20 Gb or smaller, FAT32 will generally be faster. For drives that are larger than 20 Gb, NTFS will generally be faster.
I have two HD's in my computer and both of them are running NTFS. I haven't seen NTFS screw up as much as FAT32, especially when the HD is almost full; FAT32 has a nasty problem where it will cause 100% fragmention for almost no reason. My reccomendation: go with NTFS.