Hi Kyle,
I have looked at the photos, here is what I see,
The Zener diodes appear to be backwards, the end with the band should be connected to the input.
Jumper settings:
COM = GND
Pins 2-9 = Inputs
Pins 2-9 = PullUps
These are what I expected
Pins 10..15 = PullDown
Is this what you want? What are you connecting to these?
Check the voltage on the encoder inputs, They should switch from 4.7V to less than 1.6V. Lower than 1V would be even better.
John