I would have thought it must be to do with the software environment, after all you have tried with the hardware. Have you gone through and disabled every piece of software you can think of?
Also, have you got the DVD drive set to DMA on both systems, and have you got the Via 4-in-1 drivers up to revision? - these make big difference to IDE performance. Have you got the DVD on a seperate IDE channel to the main HDD?