I have had similar problems with an Asus A7M266-D motherboard with multiple
kernel versions (2.2 through 2.6, I think).
From what I've been able to gather, my motherboard's IDE controller (AMD
768?) is buggy, and the Linux kernel doesn't do whatever the Windows
kernel does to work around the problem.
(I can't run the disks attached to the onboard IDE controller at full
sped (i.e., with DMA on) or I get extreme filesystem corruption in Linux.
Under Windows, I can run a seemingly full speed without any data-
corruption problems.)