MS says (and I believe it) that the only way to run chkdsk /r with reliable results is to have the system in a "static state". If you just run plain chkdsk with no options from say a command prompt (or something like that) you may get messages indicating a problem, maybe not, different problems in two different runs, etc. In other words, sort of iffy. I think you are running chkdsk /r from bootup, so that is okay but I wanted to make that clear.
There are two ways to achieve a static state:
Boot into Recovery Console, or use chkdsk /r and answer in the affirmative to have the chkdsk run on the next reboot - before XP loads all the way.
If you run from RC, the results are on your screen.
If you do the latter, the results are in the Event Log as I indicated before.
I don't have much SATA drive experience and can't test, but I know what can make an IDE drive perform poorly for an unobvious reason. Maybe somebody will help me understand if this logic the same with SATA drives or spur another thought.
One popular reason a HDD might be slow is that it has changed from a DMA (fastest) access mode to PIO (slowest) access mode. You would like DMA mode, and that is normally how things are, but if you have had some HDD errors, XP will switch it and not tell you (except in the Event Log if you are looking for it). Of course you should figure out why and fix it, but we can check anyway.
If you are using IDE drives, use Device Manager to verify the transfer mode of the IDE channels is set to something like DMA if available (depends on your hardware) and not the slower PIO mode.
DMA is the fastest, PIO is the slowest.
This is easy to check and generally easy to fix and the mode would not have changed by itself, so if it has changed to PIO, change it to DMA and then figure out why it changed and fix it.
To launch the Device Manger console, click Start, Run and in the box enter:
Expand the IDE/ATA controller section to see your IDE channels. Right click each, choose Properties, and for each channel that has an Advanced Settings tab, determine the Transfer Mode. There are usually 4 channels to check in a desktop, maybe fewer for laptops.
The fastest selection will be some DMA selection (usually: DMA if available). If it is PIO, change it to DMA.
If you are not sure about what you see post back for help and advice.
Follow this up with a reboot to make sure any changes stick.
What may have caused the change? http://support.microsoft.com/kb/817472