On my SabreSD (quad) board, I plugged in a RealTek-based mini-PCIe ethernet card (StarTech ST1000SMPEX). The card is detected fine in u-boot.
On my TechNexion board, I plugged in the same card, but the card is not detected (same version of u-boot, 2014.07).
I compared the two dev boards, and corresponding software, I discovered one main difference: The SabreSD board has a Power-Enable GPIO that controls a load-switch to the mini-PCIe slot. The TechNexion doesn't have it. So, I tried disabling the GPIO on the SabreSD board to see if that was the problem. Sure enough, u-boot failed to detect the card.
In my understanding, PCIe should be able to work just fine without that GPIO, since it is really just intended for hot-plug capability. Is that not true? We have a custom board that doesn't have a power-enable, and I can't communicate over PCIe.