If running a PWM timer and you issue a pause(), the pin may be left HIGH. If you are using PWM to limit power through the pin, then leaving it HIGH may not be what you want. I'm not sure what the appropriate fix is. After the pause() I added
setMode(TIMER_CH4,TIMER_DISABLED);and before the resume(), I added
pwmtimer.setMode(TIMER_CH4,TIMER_PWM);and that seemed to leave the pin LOW during pause.
On Arduino, I disable the PWM pin for a pause:
TCCR2A &= ~(_BV(COM2B1));