I've experienced a somewhat similar thing but only happens when idling along at night with all the lights on. If I speed up or turn off some lights the problem goes away. I've attibuted it to my boat being older (89 Comp) and perhaps the altenator/associated electrical system being a little tired. I've chaulked it up that the Perfect Pass needs a certain voltage/amperage and if it doesn't quite get it shuts down to protect itself then once the power level is normal it will start right back up similar to what happens when you start the boat up.
Do you have an older boat or perhaps running a large stero system? Might be something to experiment with. Alternately, just call Perfect Pass (902-468-2150) or email their tech support (
[email protected]) and I'm sure they will help you out.
Mike