A couple of things pop in my mind:

1. The mobo underclocks the CPUs too agressively, look at the "Cool'n'Quiet" BIOS setting (it shouldn't though, given the load). Issuing 'lscpu' on a terminal will show you the current MHz.

2. The memory modules might be too slow. Replace them with a couple from a 'fast' rig to see if it makes any difference.