Some additional info on this:
The issue is caused by the imx6 PCIe Root Complex which is not properly
configured on boot.
The subordinate should be set to 0xff (maximum bus nr that is reachable
downstream)
lspci -v:
[ Node 3 | node-3 ] lspci -v
00:00.0 PCI bridge: Synopsys, Inc. Device abcd
Upstream commit "PCI: Do not allocate more buses than available in
parent" limits the amount of busses being allocated upon scanning the
PCIe bus. [1]
This commit was introduced in kernel 4.9.71
This breaks PCIe scanning on the Gateworks Ventana, causing no devices
to be found.
Temp fix this by