I wonder if this could be to do with Windows falling back to PIO disk access instead of using Ultra DMA x?
In Device Manager, go to the IDE interface and check out the properties for the Primary IDE - is it set to "Use DMA if available"? And what mode does it say it is using?
If it's PIO then that's the problem. You will have to hack the registry if you need to force it back to DMA.
Windows XP attempts to use the fastest hardware mode available, until it encounters errors reading from the disk (or writing to). It then falls back to the lowest mode without errors - or the lowest available (PIO), whichever happens first.
Problem is, once you fix the errors (chkdsk /R), windows DOES NOT reset to DMA, even if you set it in Device Manager. Hence the need to manipulate the registry entries.
A couple of things you can check to confirm that disk access mode is the problem is to look at the Event Viewer / System log - look for ATAPI / Disk errors and / or warnings, and also to look for a high CPU utilisation by Hardware Interrupts.
Of course if a disk has initially had problems, it is usually a warning that the disk is not long for the world, so BACK UP and / or clone the disk and replace it.
SD