Hi
I am not sure if I understand your question 100%, but yes, Ground potentials differ.
You always connect the Ground Crocodile clamp of your oscilloscope probe to the same circuit where you want to measure signals.
If you want to measure the voltage of a battery, you would connect the GND clip to the negative terminal.
If you want to measure something that is powered by a bench supply, you connect the GND clip to the negative terminal eg.
If you have a dual channel supply, the GND potentials may also differ,
so tie them together if you want to measure signals connected to both of the outputs.
The same with interfacing boards, if two boards are powered from two different supplies,
tie the GND connections if you want to measure signals between them.
Hope it helps?
AJBotha