There are a number of contributors to problems. The first would be that with the cables that you are using, they are not impedance matched, and may not be low loss dielectric. Thus, attenuation, cross talk and reflections will close the eyes, due to loss and noise. Reflections are the result of impedance discontinuities. Our assemblies are tuned to 85 ohms, cable and PCB. PCIe Gen3 is 85 ohms. 85 and 100 ohms work interchangeably, but if mixed, you lose some signal to reflection and shorten the maximum possible length. If your performance is on the edge, that's not a good thing. Our cable is tightly coupled and uses silver plated conductors. Lower loss for conductivity, and for radiative losses coupling to ground. And we use a low loss dielectric. Impedance matching is one thing, but dielectrics absorb some of the energy too. The only thing separating these assemblies from what is used in supercomputers is the connector, and we have no control over that. The connectors are geared at being cheap and good enough, by Intel and the industry. By and large, they are.
As for crosstalk, our cable exhibits less than -40 db of crosstalk. Crosstalk can occur at the termination, since the shielding has been removed. We design the PCB termination and stackup to minimize the effects. Again, the other cable is not shielded, so there could be considerable cross talk along it's length. Between attenuation, crosstalk, and reflections there may be no eye at the far end. So for dual GPU, I think it is simply a cable performance issue. The other cable assembly was probably designed with PCIe Gen I in mind. I have seen some that advertise Gen 2, but the longest that I recall there was around 6 inches. And the prices were considerably higher than Gen I.
