Well, where to begin. I suppose first to show you the specs so you know what hardware I'm running.

http://valid.x86.fr/rhahw8

It started initially with major DPC latency problems when playing something as simple as a video file. I reinstalled both attempts on Windows 8.1 and finally Windows 10 currently. I've put all the drivers in from the ASUS website, I've updated the BIOS to 0601, I've reseated the graphics cards and tried one at a time in different slots (specifically just 1 and 3).

The current problem, while the DPC latency issue has disappeared I'm unable to get the performance I'd expect out of my Titan X's. Only from slot 3 which according to GPU-Z is x16 however it's 1.1 instead of 3.0 regardless of GPU load.

When both GPU's were installed, the primary GPU read as PCI-E 2.0 x16 @ x4 2.0 at one point, x2 at another point (yes both times under load) but since then it's read as x8 3.0 I believe after I updated the BIOS from 0502 to 0601 beta. I've reset the BIOS settings to their default values and I've ensured no overclocking was being done on the CPU or memory.

When I tried a single GPU in slot 1, it read as x8 3.0 instead of x16 3.0. Both GPU's read the same.

When I tried a single GPU in slot 3, it read as x16 however at 1.1 no matter GPU load.

The previous motherboard I had, the ASUS X99 Deluxe, didn't exhibit any of these issues. Could I have a bad motherboard or have I missed something :(?

P.S. The only power I haven't connected is the EZ_PLUG below the graphics cards. My understanding is that this is only required when there's some serious power requirements from using multiple graphics cards (e.g. 3+ I'd assume)?

Thanks in advance for any help offered.