Okay, so I'm not the only person having the controller problem, and what's more, the IDs for F-Zero and Mario Kart have changed:
F-Zero ID = GGE6E
MKACP2 USA = CNLJ82
Someone, after a bit of fiddling, managed to add credits and play it, but for me, with version 4addd0f7d5, I only have a controller problem with F-Zero AX, and I'm not the only one.