I almost forgot I had this problem.
2 years ago I bought a 3200+ s754 CPU and until 6 months or so ago it was running 32bit version of Windows XP pro with no problems.
6months or so ago, I installed XP 64bit edition... everything worked ok apart from freakin 3com being a bunch or retards and not supplying drivers for my PCI wireless NIC - screw you 3com ;-) Anyway because of this I decided to put 32bit version back on... I formatted my system partition and proceeded to reload XP.
Once 32bit XP pro was installed again, everything was fine apart from every so often (fairly regularly) when the hard drive was doing some work, the PC would completely lock up for over 30 seconds.
I couldnt figure out wtf was going on, and reinstalled (after formatting) another 2 times but never solved the issue. THe only solution was to put XP 64bit back on - which I am running to this day.
So it seems my system was fine running 32bit XP, until I installed 64bit XP and since then it freaks out when running 32bit XP and will only run smoothly on the 64 bit edition.
Did you install all of the Windows updates after reloading the 32-bit version? Maybe there was a bug fix that the 64-bit version natively has but the 32-bit version doesn't. (Well, I'm sure that there are plenty of those, but maybe that's the reason.)
......Anyway because of this I decided to put 32bit version back on... I formatted my system partition and proceeded to reload XP.
I think that may be the issue - there were some xp64 files left on your NON-system partition.
Try reloading/reformatting the system partition again, only this time get rid of any 'common' like folders out of the Program Files on your other drive (or drives).
or better yet, backup data on your non-system partition and reformat the whole setup.