2012 Mac Pro (GTX980Ti) [1st,12C,E] + GTX 780 Ti x3 @ 64Gbps-PCIe (Cyclone Backplane) + macOS 10.11.6 [hoeveler]
@hoeveler, Interesting, I wonder if you just had bad luck or if you were pulling too much out of the PCIe slots and there was not a proper limit set/negotiated. PCIe slot power limits are definitely a thing, as I found in my project I was getting major throttling due to them until I hooked up external power to the slot through an adapter. I found PCIe slot power was limited to around 25w in my case for example. I wonder if your board somehow allowed it to pull too much and it popped something? I'd think for a backplane of that quality that would have been addressed properly though.
I think it was physical/mechanical. The PC board isn't built like modern motherboards for flex-reducing / metal fortification along the PCIe slot to reduce flexing from these massive/heavy modern GPUs. I had it stacked and though it was mounted in an open-air case, there was a little bit of flex, and I think the PC circuit board developed a micro-crack. It would click in and out of connection if the GPU was gently wiggled. So it's not due to the power limits but a self-protection circuitry I think.