I wonder if the forum software can be made to handle correctly tabulated code?
Don't bet on it. FWIW when cut and pasted into one of my editors it looks fine.
Unfortunately that hasn't helped my spot any errors 
EDIT:
It seems to me that it's either in the timer PWM code or the PID code. Can you verify one way or the other by checking that the timer is getting a correct value, say printing the value.
I guess that means waiting a few days.
Another option is to apply a sanity test to the PWM value, might be difficult though of the range is 0 to 100%.
Rob