A follow up to close this. I still don't know exactly what was causing this issue, but I suspect it is something to do with the Arduino wrapper and the implementation of the 8 "Low Speed" PWM channels, as I was only getting problems on those channels and only when I was also using a separate timer i...

The last 3 PWM channels are at a steady 1.6V.
PWM9 pin 15
PWM10 pin 25
PWM11 pin 33

If I swa p pin configs around then the problem stays with the PWM channel rather than the pin

I'm getting some strange behaviour with this, that maybe somebody could help with please? The purpose of the code is to cycle sequentially though 11 different configurations, with each configuration (I call it a crank position) calling for 3 out of 11 PWM channels to be activated. A different 3 chan...