Failed to Enumerate Stratix IV GX FPGA Development PCIe Board on PCIe 3.0 Bus

Sounds like you had a good idea to download the .sof in BIOS mode ... there is an inherent race condition if the FPGA has to load and be ready when the slot reset is deasserted. I had problems with that and one powered up and FPGA loaded, I had to do a worm restart of Windows which if you are lucky, will not cycle the power, just reset the slots and re-enumerate the PCIe buses.