I have a i7-5930K (40 lanes), a GTX Titan X on the Rampage V Extreme/U3.1 and a Samsung SM951 in the M.2 slot. The motherboard revision is 1.01 and the BIOS revision is 1401.

Some background:
When using a 40-lane CPU, PCIE_X8_4 shares bandwidth with M.2 x4 slot and can be run at x4 mode, according to the manual (page X). In the BIOS option "Advanced\Onboard Devices Configuration\PCIEx8_4 and M.2 Configuration", there's a dual-choice setting [Auto] or [M.2] to let the user specify whether to prioritize either PCIE_X8_4 slot or the M.2 x4 slot. If [Auto] is chosen, then the M.2 x4 slot will be disabled, allowing PCIE_X8_4 to run at x8 speed. If [M.2] is chosen, then the M.2 x4 slot will be enabled, and the device in PCIE_X8_4 will be forced to run at x4 or less speed, according to the description of this specific BIOS option.

Now the bug: If a PCIe device with more than four electrical lanes has been plugged into the PCIE_X8_4 slot, the bandwidth sharing with M.2 option will disable the device completely instead of forcing the device to run at x4.

Here's a quick way to reproduce the bug:
0. Make sure you have a 40-lane CPU on your motherboard.
1. In the BIOS settings, set the above option to [Auto].
2. Plug a PCIe M.2 x4 SSD in the M.2 x4 slot, and install a bootable operating system on it.
3. Plug a PCIe x16, electrical x16 GPU in PCIE_X8_4 slot.
4. Start the computer. The GPU in PCIE_X8_4 slot will have video output, but the M.2 SSD will not appear in the BIOS boot list. This is intended behavior because the M.2 device is disabled.
5. In the BIOS settings, set the above option to [M.2].
6. Start the computer. The GPU in PCIE_X8_4 slot will have NO video output. This is NOT intended behavior: it should run at x4 speed. If you have another video card, you can use its video output to go in the BIOS and confirm that the M.2 SSD reappears in the BIOS boot list.
7. Remove the GPU in the PCIE_X8_4 slot, and use adhesive tape to mask pin 33 to pin 82 (refer to http://en.wikipedia.org/wiki/PCI_Express). After doing this, it will be forced to run at electrical x4 speed.
8. Re-plug the GPU in the PCIE_X8_4 slot.
9. Start the computer. The GPU in PCIE_X8_4 slot's video output is now back, and the M.2 SSD will appear in the BIOS boot list. If you boot into an operating system, you can use various tools to confirm that the GPU indeed run at x4 speed.

The above behavior would ONLY happen if the BIOS disables devices plugged into the PCIE_X8_4 slot that has more than four electrical lanes connected when it is sharing bandwidth with a prioritized M.2 slot, instead of forcing the device to run at x4 speed as advertised.

I hope this will be fixed soon, either by explicitly forcing the device in PCIE_X8_4 to run at x4 speed when M.2 x4 is prioritized, or add an option in the BIOS settings to enable this behavior.