Ok my troubleshooting is over on that factory encoder. It fell apart. After taking it off the circuit board, the one I had appears to be this one.
Datasheet,
Digikey catalog (top: figure 4)
It's probably not exact, because the OEM one was 30PPR and this one is 20PPR, but I can't find 30.
I notice that it was laid out, in circuit, more like the sample circuit shown, with the switched common and capacitors (but I cant find the 10k resistors on the board that the encoder was on).
I suppose there are some reasons why you wanted to switch + vs. com.
Well, I'm going to order a few more of these and give it another go.