Isolated, Non-isolated Power Supply effect on running Hardware

I've a hardware to run a motor. It consumes max 20A current at 16V.

I'm using a non-isolated power regulator for powering my hardware setup. When the power is turned ON, the motor turns on but does not rotate (with load and without load).

I connected an isolated power regulator and turned ON the hardware setup. It worked fine. I realized that the non-isolated power regulatior's earth is interfering by creating a ground loop and not allowing current to flow through the motor to run.

Later, after 6 hours, I used the same hardware on both isolated and non-isolated power regulator. Voila! Everything worked fine, the motor is running like it is supposed to be both on load and no-load condition. 

 

I don't get the point here. What is missing in the first case to second one?

"I realized that the non-isolated power regulatior's earth is interfering by creating a ground loop and not allowing current to flow through the motor to run."

So what did you do when you realize this?

In my point of view, the only difference is with regards to safety. There will be an electrical connection between the input and output when its non-isolated. That might cause problems if not address properly.