My only theory would be that the defective MOBO did not feed the GPUs enough data or power, so they were throttling off 100% and were running cooler.
On my 6990s the current draw went up by like 40% after i added water blocks to them and so they stopped throttling back. in my case  they were throttling back b/c of temperature, in you case might be b/c of faulty MOBO. GPUs do get some of its electrical power from PCIe slot, so if mb could not give its full 150W spec for PCIe2 slot the gpu would work slower and run cooler...