I recently had a similar problem. After endless days of scans for viruses, malware, rootkits and hardware diagnostics which all turned up negative, it turns out that CD had reverted to PIO setting instead of it's normal DMA. This was causing the system to spend much of it's time handling hardware interrupts.
Easy enough to check out:
- Right Click My Computer
- Click Properties
- Click Hardware Tab
- Click Device Manager
- Find IDE Controllers in list and double click
- Double Click Secondary IDE Channel
- Click Advanced Setting
If the transfer mode is set to PIO that may be your problem. Check out
Lame Hard Disk. Do NOT do the Quick Fix, instead scroll down to Item #6 and do the fix manually. If you're skittish about changing the registry, create a restore point or use
ERUNT to back up your registry.
No guarantees, but just maybe.