is your theory that the PWM output will eventually stop?
Not so much my theory, but my experience, yes.
It sounds so totally strange, I see no reason whatsoever that it should stop, but stop it does.
Maybe put some extra serial debugs in the test code, such as what I have and I hope you have seen on my web page.
Particularly TCCR3A, that is the one that is getting changed, bit 5 from being set to being cleared.
I will do some tests on hard coding the value and writing on the Timer3.pwm(..) function just as it does in Timer3.setPwmDuty(..) function to find out what happens.
I do appreciate your help Nick, and Rob too.
Paul