well, did you look and see if the CPU's were, in fact, a matched set? You need to check the stepping of the CPU's. That could be your problem. Also, check with Tyan for any issues, check the BIOS and make sure that you have the MPS version set to 1.4, and make sure that you don't need any kind of VRM to run duals. Then see if you install another OS if the same problem comes up. I doubt your problem is with e-smith (linux). Loading another OS may give you more info on the problem, though. This is more than likely a hardware issue and not software.
Hope this helps!