Just for other people that find this topic after hours of troubleshooting: this problem unfortunately also exists on the Supermicro X10SRL-F. If it wasn't for this post I probably would never have found the issue (except removing PCI-e cards which would have been a logical next step). In my case disabling the OpROM didn't help and I had to remove a couple of HBA (LSI 9211-8i) cards. It worked with only two HBA cards left.
Really frustrating bug. I hope someone finds this post faster if he/she has a X10SRL-F.