We have reproduced your setup here. We have used an RevPi Core 3 and an AIO module that is configured using 0-20 mA for Output1 and Output2.
The wiring is setup as follows: Output1 is connected to Input1 and Input2; Output2 is connected to Input3 and Input4.
We have created the attached program "aiotest.py" that creates a sinus signal and prints out the values. You may run and sample the data by the command
chmod +x runme.sh; ./runme.sh
Our result is that no outliers apparent so we have the guess that the wiring could be the root cause of the suspicious behavior.
Probably the GND circuit could be enhanced. GND input and output must not be connected because differential inputs can not work otherwise.
Idea: Separate the two outputs from each other