I recently upgraded from an 8.4gb disk to a 2.5gb Western Digital ATA-66 7200rpm drive. My motherboard does not support ATA-66 but I don't think the drive is actually trying to use ATA-66. Everything works perfectly but that drive is using MS-DOS Compatibility mode.
I have the old 8.4gb disk slaved, and it uses the protected mode drivers with no problem.
I have booted into safe mode and tried to remove the primary hard disk controller (dual fifo) but it says to remove the parent device first (Intel PCI Bus Master IDE Controller). I tried that but after removing the parent device I still could not remove the controller. After rebooting it autodetected the PCI Bus Master IDE Controller and then we were back to MS-DOS Compatibility mode.