I was able to fix the order by disabling all three in device manager and then enabling the real ones one at a time leaving the phantom one disabled.
I was able to tell which one was being enabled because the LED on the PCB lit up when enabled.
Upon restarting though, it insists on having player 1 & 2 swapped.
So I guess I'm rewiring.
Back when I initially installed these hacked pads, I thought windows put them in order based on some internal ID (as opposed to directinput controllers which go in order they are installed).
It seems windows 10 likes a different order than Vista.
EDIT: upon a second restart, P2 pcb didn't start, which is what P1's was doing when it was being flaky. Seems to be a windows issue since it's now the other PCB. (whichever one shows as P1 before failing to power up on the next restart.
I'm going back to a keyboard encoder.