I had this exact same problem. There is a setting for your hard drive called DMA, basically every harddrive/cd-rom is DMA compatible for the last like 10 years, but for some dumbass reason the folks who put together my PC didn't have it on, it was such an obvious fix that I didn't think to look for it.
To check if you have DMA enabled:
1) Right click on "My Computer" and click properties
2) Go to the hardware tab and click "Device Manager"
3) You want to find your Primary IDE controller so look for an item with something similar to "IDE ATA/ATAPI controllers".
4) Double click your "Primary IDE Channel", go to the "Advanced settings" tab and see what the "Current transfer mode" for device 0 is. If it says PIO then DMA isn't enabled. To enable it click on the "transfer mode" drop down and select "DMA if available". Then go back to the device manager screen, right click on the primary IDE channel and remove it. Reboot windows and when it restarts, it will reinstall your IDE channel with DMA enabled.
That should clear it up, you can check your secondary IDE channel as well, thats usually the CD ROM. Enabling it should give it better performance.
Of course if DMA is already active, then I have no idea what the issue could be.