If found on MSI 890FXA-GD70 MB that in moving cards around I got aticonfig all screwed up. Nothing seemed to fix until I reset (not flashed) bios. Then cards were back in the right order. I think BIOS may have something to do with the order that OS sees the cards in.
Naturally, see the Init Display First
The order cards are initialized in is reflected in the BIOS device map (that measly 64k of memory which tends to get clogged up with the unnecessary mobo "goodies").
Some better-behaved bioses actually allow you to choose PEG1 or PEG2 (as in P
raphics) as the primary device.
I've yet to see a bios allowing me to select any PCIe slot for the primary GPU.