I used to fly as crew on the B412EP in the UK and yes the noise is quite normal when completing the governor manual checks during the start up functional checks. I understand that it was not a problem as when completing these checks as the power loading was light (other engine driving the rotors and the engine being checked is at idle at the time of changing from manual to auto or vice-versa)
The only time I've heard the noise in flight ( and only on a couple of rare occasions) whilst the engine is in auto governor mode was at the bottom of a PFL (autorotation) when recovering to S&L flight whilst pulling in power (going from power on auto to power on flight). We were informed that this was "pop surge" and the a/c were to be landed on and shut down (I believe this was an instruction from Bell) and then subject to engineering inspections. Exactly what inspections, I dont know as I'm not an engineer but I suspect it is something to do with transient torque spikes as both engines are under load at this time.
Our a/c were equipped with the PT6T twin packs.
Hope this helps