Nick,
Try different values. In particular, extreme ones (eg. 0, 1023 or close to that)
On the board running the program the values do go from 0 to 1023 and anything in between.
When the PID is not putting out any output, it is zero and that is what is fed into the function Timer3.setPwmDuty(..).
Then when the PID is wanting maximum output, that is 1023, that is what is fed into that same function.
So, the value going into the function every 100mSec is more or less constantly on the move.
The problem is not to do with the value I provide to the function I am certain, more that Timer Control Register 3A (TCCR3A) becomes cleared to zero at some point in time.
Paul