I have figured it out. The MSI Z270 Tomahawk disables PCI slots 2 and 5 when slots 3 and 6 are occupied. So it turns out it is impossible to run 6 GPU's using the PCI slots on this particular motherboard. I have returned the motherboard and purchased a new asus prime Z270-a. Going to try with this one now.

Hi everyone,
I'm just trying to set up a second mining rig but I have encountered an annoying problem that I was hoping someone might be able to help me with.
When I connect my GPU to a particular PCI-e slot, it is recognised by the motherboard as being connected into 2 PCI-e slots. Here are some pictures that might help explain what I mean;

(only one GPU connected)

(Motherboard thinks 2 GPU's connected)

If I plug another GPU into that second PCI-e slot it inst detected. Both PCI-e slots work individually, just not at the same time.
This same problem happens with another 2 PCI-e ports on the motherboard, so the maximum amount of GPU's I can run is 4.

I also have 4G decoding enabled and have tried Gen1, Gen2 and Gen3


My motherboard is MSI 270 Tomahawk with Intel Celeron G3930
Im also using GTX 1060 cards.
I have been trying for the last 2 days to find a fix but with no success, so I thought I might ask if there is anyone out there who has had a similar problem.