All my HDD are on SATA--nowhere near any IDE channels. My mobo--Intel 925XCV--only has one IDE channel, so that's why the add-in Adaptec card. (Mobo IDE already has two burners on it--NEC 3520 and LG 4163.)
As far as what modes they should be, I apparently don't have any say in the matter, as the Adaptec card decides what mode to set each drive, and there is no way to change it.
The only thing I can think of to do, is put one drive on each channel, instead of both drives on the primary channel, and see if that makes a difference. Do you think it will?