Fat 32 WILL support partitions up to 2TB .... 2000 and XP cannot CREATE a partition greater than 32Gb but can read a disc up to 2 TB (the work round is to use a 98se boot disc to create the partitions.
(
http://www.mcmcse.com/windows_xp/guides/filesy stems.shtml)
6.02Gb is a red herring ... fat 16 is <2Gb - the old bios int 13 limitation was 7.8Gb.... (lba is 7.8-132Gb, lba48 is 132->)
I think the problem is just down to the bios not autodetecting the swapping between the 6 and 40Gb discs
look for a "detect my drive" option in the general settings ... and you'll get the full 40Gb back.
It is a good idea however to have a dedicated system disc ..and seperate data/proggy partitions ... just in case!
Add another partition to the machine and you could have a dual boot machine
Install 98 then xp
and remember 98 can't read ntfs