Hi,
With the new wiring I don't expect GND problems anymore...but "knowing" is better than "guessing", thus I also recommend to measure it.
If I remember right you have a 4 channel scope.
With one measurement we can verify a couple of things.
I recommend:
* connect all channel cable GNDs to the copper foil of your microcontroller board.
* connect channel 1 to the GND connection of the power PCB
* connect channel 2 to the VCC of the power PCB
* connect channel 3 to the high side signal after the level shift circuit
* connect channel 4 to the low side signal after the level shift circuit (same half bridge as channel 3)
Klaus