Had the same problem with two 200GB harddisks, with a c: partition and several other partitions, all full of data, most of it is lost now.
Think this is the cause:
http://support.microsoft.com/?id=303013
Somewhere half way through the page there is this warning:
Warning Data corruption may occur if either of the following conditions is true:
• You use this registry value to enable 48-bit LBA support in the original release version of Windows XP Home Edition or of Windows XP Professional.
• You install an earlier version of Windows on a disk partition that was previously created by a 48-bit aware operating system, such as Windows XP SP1. And that disk partition is equal to or larger than the current addressable limit of 137 GB.
After a motherboard replacement I had to reinstall XP. I did this with a clean XP without integrated service packs (note there are easy tools to create WINXP CDs with integrated SP2, look for autopatcher from neowin, and pebuilder).
By now it was too late as files were corrupted.
Installation of SP 2 did not help, other then XP trying to fix corrupt and orphaned files.
The data I had on the harddisks is corrupted to an extent I can't determine. Basically I'm considering this a full loss.
Next time I need to re-install I will disconnect any large harddrives. Then I will install XP on a 80 GB or smaller harddisk and install SP2. Or install XP with SP 2 already integrated.
And only after that is complete will I reconnect the 200GB data disks.