Thank you for the report.
Unfortunately, I have been unable to reproduce the issue.
I have failed to communicate this clearly, so just to make sure. The two electric poles of the transformator do not connect to internals of the transformator. They only carry the circuit wires just like normal electric poles. The internal pump is not aware of the circuit wires connected to these poles. To control the transformator, you must connect circuit wires directly to the pump portion of the transformator.
In testing, I did notice that the quick power on/off is not working properly, so I will be looking into that bug.
I will continue to try more combinations, attempting to reproduce this issue.
Are you willing share your combinator setup?
Are you using the Overhaul (wiring rules) or the transformator only option?