So one more thing that I didn’t do until now was to take a look at the Odrive schematic. It looks like it already has the pull-up resistors that would be necessary for an open collector type of encoder output. Do you have a multimeter available? If so, are you able to measure 3.3V on the A and the B pins on the Odrive with the encoder disconnected?
Which power pin do you have the encoders hooked up to? 5V or VCC? VCC is only 3.3V on the Odrive which may not be enough to power your encoders. If you are currently connected to VCC, on just one of your encoders it might be worthwhile to try switching to using the 5V power pin instead to see if that fixes your problems.