Hi Dale,
I'm in the same boat as you in that I can not get the encoder, a AMT103, to display or process the RPM pulse in the ENCODER(Lathe) mode. I get very steady and very accurate reading in the INDEX(Lathe) mode only. I also get very clean A, B & INDEX scoped pulses on the RJ45_7 pins and have been trying PK Pins 8, 12 & 13 as shown in the Pokeys Manual. My next step is to hard wire the PK pins direct.