I am having the same problem. I have isolated it to the ATA HDD driver switching back to PIO mode from DMA. this means the processor has to manage all the I/O and results in a huge increase in processor utilisation due to interrupts.
Go to your device manager select the IDA ATA / ATAPI controllers group
select the ATA channel for your HDD or DVD, select advanced setting tab and check the "Enable DMA" check box then click ok.
This re-enables the DMA for the HDD channel and frees up the CPU.
My problem is that the mode gets reset to PIO mode each time I reboot my windows 7.
After research I see that windows 7 will do this if it detects over 6 CRC errors from the drive (also if a badly scratched DVD is read) Google "ATA PIO problem".
I don't use my DVD and HD Tune Pro tells me I have not CRC errors or bad sectors on my HDD.
I have also checked the system events (administration tool) using the event viewer and I did have 4 disk controller errors which I am assuming is causing windows to switch back to PIO mode.
If this is not the problem there is a very good post about using the Microsoft Windows performance tool kit to find out which drivers are using up CPU instead of using a trial and error approach.
http://blogs.msdn.com/b/peterwie/archive/2008/10/06/measuring-dpc-time.aspx
Hope this helps