In that case, what you are experiencing is expected behavior.
If your motherboard doesn't have a metal retention clip on the CPU 2 socket, it won't take the omni path Xeons in that socket.
It's not Supermicro's fault. Not to mention that the omni path xeons are not supported since many years...
Do both sockets have the metal retention clip?
If so, the only solution I can think of is swapping the QN3E in the socket CPU 1 for an 8160 QS or retail and keep the other one in the CPU0. For some reason, the motherboard won't take two CPUs with omni path fabric.