Update: One of the reasons I chose this problem to investigate is that I wanted to better understand the process path. It was unintuitive to me that a gear box on the B side could be driven through the lever with a pulsing force in the A Side.
What I just discovered is a fix to the inconsistent explorer results. By ching the Wheel and axle B to work in the negative direction, the B scope matches the results explorer.
I'm looking forward to your thoughs on this topic and still looking for help on my flatlines though.