Encoder(maybe) issue.

No. There is a cable coming out of the cabinet with the zeta in it and on the end of that is a female db9 and on the end of the encoder is male db9
 
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.
 
i've used a scope once or twice in my life not exactly a pro at it.
the 'scope we have her is a tektonix TDS 2012B.

when i hook up and do the measurements simulatanoues for max and mean and i'm getting 4.88-5.36 volts.
 
Should be 50 millivolts. A video of what you should see here.
Follow instructions here for printing to a flash drive. Post a JPG and I'll look at it.

Connect 'scope to another Zeta or other 5 volt supply to see what's normal.
 
Just so I'm hooking it up right I'm using channel 1 autorange turned on. The clamp that attaches to the side of the probe is clamped onto the shield of the cable which is connected to the shield terminal of the encoder plug. I was able to connect the probe to the screw terminal of +5v terminal. I will look at the video when I get it. Also the zeta drive itself was so hot o could barely touch the heat exchanger fins
 
Leave trigger where it was set with autoset.
Are all photos from the 5V terminal?

Manual shows an isolated ground. Connecting to the encoder shield connects you to chassis ground. Try connecting ground of the probe to terminal 4.
 
I had to bring the 0 point down so you could see the line with the same settings as when i bench tested it. The machine is running so they can get an accurate range of the variation so i won't be able to bench it again until tonight.

20160114_154904_resized.jpg
 
You were set to 1 Volt per division. With the line in the middle, it moved up 5 divisions. That's because you are set to DC, and the signal is 5 volts.
In the channel 1 menu, change Coupling to AC. In Vertical, Turn Volts/Div down to 50mv or so.
 
It should look like the yellow trace in post 19. Those spikes are disturbing. Looks like something is arcing. Now we know where the extra counts are coming from.

Repair or replace the Zeta drive.
 

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