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if you: 

1. Disconnect the encoder

2. Change the index input to TTL mode
(W1 left)

3. With LinuxCNC running and halshows "Watch" tab showing
    hm2_7i96s.0.encoder.00.input-index, does the state of
    hm2_7i96s.0.encoder.00.input-index change when you ground
    the IDX+ input (TB2 pin 13)?

My wiring is good. I followed the MESA7i96s documentation. I think everything is correct.
I've tested 5 RS-422 encoders with phase A+,A-,B+,B-,Z+,Z-. Or maybe my MESA board isn't working properly. I don't know how to get out of it

Good point I forgot to mention the specs
Current is 3A. Resistance is 1.3 Ohm
Holding torque 3 Nm
I run them with a 36v power supply.

O guess that about no voltage specification is a good point you don’t know what transistors are in there.