Ok, figured it out. There's a really tiny (like literally) footnote in the motherboards manual that says the bottom 16x slot shares its bus with the 1x slots. If there is anything plugged into there then each PCI-e lane it uses shuts off one of the 1x slots.

Armed with this knowledge I could get 4 cards working in that motherboard. Maybe it could do 5 but I'm out of risers and really not in the mood to fuck around with it any further.