Onboard Intel X540-T2 disappears when connected directly to another 10GBe X540-T2 PCIe Device

Hi Intel Folks I have a very strange Problem:

I got a Supermicro X9SRH-7TF Mainboard which comes with 2 Onboard 10GBe Ports through an X540-T2 Chipset. For about a year I had those two ports connected to a 1GBe Switch and everything was just fine. I got another Server which I recently added a 10GBe X540-T2 PCIe Card. I initially only connected the Servers physically without assigning IP Addresses within their Windows Server 2012 R2 OS. Then I was away for a week or something, came back and both 10 GBe Onboard Ports first showed up having trouble (Error Code 43) until after some trying to reapply the Intel PRO Driver Package (v18.7) they degraded to unknown Communication Device in the device Manager.

This is all I have from the Windows Event Logs: Log Name: System Source: Microsoft-Windows-UserPnp Date: - Pastebin.com

The Server with the PCIe 10GBe Card shows as connectivity "Disconnected" on the 10GBe Ports since the first server decided to not like those 2 Onboard Ports anymore.

This also is reproducable: In the meantime I've exchanged the Mainboard since I thought those onboard ports are screwed up but it's the same with the new Mainboard. I'm not sure where to look for this Problem (BIOS, Drivers, something else?) so I hope for your help asides my request towards SuperMicro.

Thanks