If Windows uses PIO mode instead of DMA, it probably have slowed down due to reading errors. To fix the slow-down, find the registry key:
This contains the subfolders
0001 is the primary IDE port and
0002 is the secondary. But
watch the entries in there and you'll get the idea.
The important values are
MasterDeviceTimingModeAllowed as well as
SlaveDeviceTimingModeAllowed. Delete the keys and reboot. Windows will re-detect the speed and should be back at
full DMA speed.
Usually, this should be fixed since SP2, but it seems to not work everywhere. You could try to force a retry by adding
ResetErrorCounterOnSuccess with a value of
1 to that key.