The Native R2 Chassis have problems with a mismatch between Slot 1 and Slot 2. In case of missing PCIe Link of the CPU, insert the module into Slot4. Use the MCH Webpage, open Page “PCIe Virtual Switches”, select as Upstream Virtual Switch AMC4 and activate all radio buttons for all slots. Apply. Save. Reboot.

This backplane requires a config update: look here