Until recently I had a Gene IV and now I have a Gene V and I'm getting the same unusual problem with both of them not recognising my GPU (MSI HD7970) when it's seated in the first PCIe slot, but both recognising it in the second one no problem.

Is this a known issue with these boards and, if so, is there a fix?

I've tried virtually everything to fix this, from clearing CMOS to reseating GPU to changing RAM configurations to disabling iGPU, but I'm no nearer a solution.