Odd motor noise

Good morning, I am building an FPV cinelifter quad with someone and we are getting an odd behaviour with the motors. We are using APD F-200 ESCs and they work perfectly if plugged into servo slot 1 or 2. The motors spool up and run as you would expect. The minute you plug any ESC into servo slots 3 or 4, the motors sound really rough and vibrations go through the roof once you throttle up. I will get a log file tomorrow but just wondering if anyone has any ideas at this stage. The FC is a Cube Orange on 4.1.3 using the Hex Mini carrier board. ESCs are set to use PWM (it did the same when set to DShot too).

Why don’t you use Dshot on the Aux/FMU outputs?

We did and it was the same with that (just translate the servo numbers over so to speak)

So this osicilloscope vid shows what is happening re PWM. Could this be a PID issue with the copter on the bench?