Interrupts can have a nasty system-wide effect when hogging CPU and it can be worse than you realize. The problem is likely that your IDE ATA/ATAPI disk is running in PIO mode, which is the slowest, due to some time-outs or errors. To check and see if this is the problem, follow these steps:

1. Go to Device Manager (Right-click My Computer>Properties>Hardware Tab>Device Manager);
2. Expand IDE ATA/ATAPI Controllers and click on Primary IDE Channel;
3. Click Properties button and select the Advanced Settings Tab;
4. If the Transfer Mode is PIO and not DMA, this is your problem;
5. Leave Properties panel open.

Quick Method

A Microsoft Knowledge base says remove the IDE ATA / ATAPI driver...

Reboot twice and then problem is gone.

Longer Method (untested)

The fix is relatively quick and painless. It requires two successive reboots. Just make sure you follow these directions all the way to the end or the problem will come back.

1. Open Registry Editor (Start>Run> “regedit”>OK);
2. Expand HKEY_CURRENT_CONFIG/System/CurrentControlSet/Control/Class/{4D36E96A-E325-11CE-BFC1-08002BE10318};
3. Highlight 0001 and click Edit>New>DWORD Value;
4. Type “ResetErrorCountersOnSuccess” and hit Enter;
5. Click Edit>Modify;
6. Enter “1” into the Value Data and hit OK.

This should fix the problem with Interrupts and make your system run much better.

Also read DMA reverts to PIO, this provides causes and other fixes.