I believe your motherboard may use the same chipset as mine (mine is an msi KT3 Ultra2, via kt333 chipset) The southbridge chip seems to be the key factor.
In my case the problem started as a lack of functionality (couldn't set DMA on my dvd), as long as both of my hard drives were on seperate cables. Once both drives were on the same cable I began having extremely frequent and random seeming crashes which eventually corrupted my reiserfs so badly (w/ my help due to hard resets) that it could not be repaired. Are your drives properly configured as master and slave?
Search your /var/log/boot.msg for the following
<4>VP_IDE: Unknown VIA SouthBridge, contact Vojtech Pavlik
Actually my mainboard has the same chipset. /var/boot/log/messages says: "<4>VP_IDE: IDE controller on PCI bus 00 dev 21 <4>VP_IDE: chipset revision 16 <4>VP_IDE: not 100%% native mode: will probe irqs later <6>VP_IDE: VIA vt82c686a (rev 22) IDE UDMA66 controller on pci00:04.1 <4> ide0: BM-DMA at 0xd800-0xd807, BIOS settings: hda:DMA, hdb:pio <4> ide1: BM-DMA at 0xd808-0xd80f, BIOS settings: hdc:DMA, hdd:pio" Seems not to be a problem in my case. What I don't understand is that dma does not work but dma and udma2 does.
PS, your reply came directly to me rather than the list so I replied directly as well. Sorry about that.
Fabian