This is probably happening at the HW level, and the usual utilities probably won't be much of a help there. I'd think a scope and a logic analyzer would be needed to solve this (and you should have those ) but you would also need to know the ins and outs of that mobo, including the chips and buses. (which you probably don't)
I'm not sure what you've done -- the first thing I'd look is all the event logs -- more often than not, if there is an issue, something will be there.
Based on the symptoms, something probably hogs some bus, or some other critical resource for an excessive amount of time, and without the necessary knowledge, pinpointing the root cause is not going to be easy.
In any case, since you have 2 identical mobos, you can exchange everything that removable and verify that they work fine in the other mobo, or not. At some point you either find a defective part, or left with the mobo, and since you've tried everything else, the mobo must be defective.--
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