I have a Mac Pro 2012 5,1. When I upgraded to Sierra a couple years ago it seems PCIe slots 3 & 4 stopped working. I later went to High Sierra and still those slots are not working. How can I fix this?
Canned air + a brush like this ; clean the PCi slots..
Also,
shut down, remove power cord for a few minutes and then all PCie cards including current GPU . .. then . . install the current GPU in a different pci slot.
Now restart using the "Three Consecutive Happy mac NVRAM reset.
IMPORTANT : It is vital to HOLD DOWN the keys illustrated below until one hears the THIRD CHIME.
Worked for me in re-setting my PCIe slots when my GPU(s) were not displaying the correct Link Speed nor Link Width.