Leave the encoder cable alone. There's no need to scope it. It's a new encoder, and I'm sure it's fine.
Look at page 11 of the Zeta manual. It has +5 Volts on pin 9 of the encoder cable. That's the pin I want to put a 'scope on, but it's difficult to access.
Look at the I/O connector. It has a +5V source on pin 6 that you can use to power AUX-P and V_I/O. I'll bet that's the same 5 Volts that's powering the encoder. Put a 'scope on it, to verify the 5 Volts is in spec, and doesn't have any noise on it.
If it's bad, replace the Zeta, or have someone replace the caps in the power supply.