There are LEDs next to each screw terminal on the PMDX-126.
Your "Encoder 1" config has step and direction signals set to "active low". That means the Step signal should be high when idle, and pulse low for each step. This in turn means that the PMDX-126 LED for all step signals will be "on", with the LED for the actual step signal getting dimmer as the motor speeds up.
The LEDs for the direction signals will (I think) be high (LED "on") for moving in the positive direction, and low (LED "off") for moving in the negative direction.
Try jogging the X axis in the positive direction. According to the "Encoder 1" configuration, the "2" LED (J4) should get dimmer as the motor ramps up to max speed, then brighter as the motor slows down. The "6" LED (J2) should be "on" (I think). Then jog the X axis in the negative direction. The "6" LED (J2) should turn off, and the "2" LED (J4) should get dimmer and brighter as the motor speeds up and slows down, respectively. Do you see this, or anything like it? Do you see any OTHER LEDs changing?
Try the same experiment with the Y and Z motors. What do you see?
Are you jogging using a pendent, or from the Mach3 screen controls or keyboard arrow keys? Not that I think this makes any difference, but I saw a reference to a ShuttlePro in your config file. I also see a "RogersPlug", what kind of plug-in is that?