I'm starting to feel like I'm a bit of a pain in the bum with my second thread in as many days but I've just had No Fault Found on the MSI X58A board I RMA'd back to you.
I simply could not get this board stable with the components I have. The same components are working happily in the original P6TD I RMA'd (the problem there turned out to be a faulty Enermax PSU) and in the same case.
Can you please confirm that you've used the same memory and the same amount in your testing? I used 2 x 6GB Corsair TR3X6G1600C8D in mine and the board would simply not function with all the memory installed (the memory has passed numerous Memtest86+ checks and is functioning fine in my P6TD.) Please note, I successfully ran a prolonged Linpack via OCCT without any crashes on this board, the faults always happened during general Windows use.
There's a thread over on Clunk's forum about the problems I was having and the steps I took to try to get the board running.