That's one problem, another is the size of the powersupply. And maybe that's the only problem, I don't see why a GPU would become unstable when using fewer lanes, all it should do is get slower.
I just bought a GTX1080ti + a similar corsair as an upgrade for my 3 year old Dell, it works like a charm.
If you have a PSU that big then that probably isn't the problem. I thought you might be using the PSU that comes with those extender boxes and they usually are very puny (250 W or so).
Yes, each GPUs has a 4x -> 16x and a 4x-4x extender, in addition to the m.2 -> PCI-e 4x adapter.
So many potential failure points in there. The sole use case is CUDA. Essentially I wanted a portable cluster with GPUs and that did the work for a couple of month. Now it's getting more serious so the switch to T630 makes sense, and I repurposed the NUCs into the control plane of the K8s cluster.
It works, but the GPUs aren't very stable at 4x vs. a normal 16x.