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:
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Class\{4D36E96A-E325-11CE-BFC1-08002BE10318}This contains the subfolders 0000, 0001 and 0002. 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 MasterIdDataChecksum and MasterDeviceTimingModeAllowed as well as SlaveIdDataChecksum and 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 a DWORD-entry ResetErrorCounterOnSuccess with a value of 1 to that key.