Have you seen this:
and are the PCie x16 lane switches on (next page) and you are using the correct slots.
Oh, wait, I assumed that was just for LED's to show where you put them on the motherboard? I'll give it a try. At the moment however even with just one card (switched to the other Titan X), I'm just getting x8. The only thing I don't have plugged in is the 4-pin molex at the bottom of the motherboard for supply extra power to the graphics cards. For one graphics card I assumed that wouldn't be needed to get x16 anyway.
Also, the GPU Post section of the BIOS still refuses to recognise any graphics cards plugged in (every slot says 'No VGA Card').
Anyway I'll try what you suggested and see if it helps.
EDIT: Let me check what you mean about the PCI-E x16 switches.
EDIT: Yes, all switches are on.
EDIT: I've decided to try putting the single graphics card in slot 3. While the BIOS says it's x16, GPU-Z also says it's x16 however there's a catch. PCI-E 1.1 x16 @ x16 1.1. Performance however seems normal for one Titan X.
EDIT: The problem was caused by the graphics cards not seating properly in slot 1 and 3, this is unfortunately caused by the SATA ports hitting on the graphics card board itself so preventing me from seating it. Putting in the very bottom slot works fine but it's only x8 and only allows me to put one GPU in. It also shows up in the BIOS. Is there any way around this I wonder?