Last year, I had something similar happening that was dumbfounding us...until we checked the batteries. Our boat was supposed to be automatically switching the batteries, but the battery that the stereo was hooked up to was about dead, but the other battery was fine, and was starting and running the boat. We were really scratching our heads, thinking either the HU or the amps were bad, but we couldn't figure it out for a while. So, based on my experience last year, don't overlook the obvious and check both batteries and make sure they are good.
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