If Windows detects read/write errors on an HDD it can automatically lower the data transfer rate of your HDD from UDMA6 -> UDMA5 -> UDMA4 etc... If the errors persist you can end up in PIO mode which will make your system run *really* slowly.
The fix is simply right click the IDE Channel in device manager and uninstall it. Reboot the machine and Windows will automatically re-install the IDE Channel in UDMA mode. Make sure you have transfer mode set to "DMA if available"