Welcome to the ATFs, teamfox. Obviously something is different. Have you tried updating to the latest chipset drivers for the mobo on the one that is slow. Sometimes the drivers don't take for both channels. Also have you checked the DMA settings on the slow one - may be set for PIO operation. Are the drive layouts the same in both? Same drives on same controller channels, etc. Do you have an 80-wire cable on one and only a 40-wire on the other. Just keep looking and thinking, you'll find the problem.
.bh.