Is this the first unit on this boat? If not, I'm guessing you did not have the issue with the unit before this one?? You mentioned that Garmin had you purchase a new transducer; did you keep the original? If so, could you temporarily mount you unit with the original TD in another boat?? You can use a suction cup to temp mount the TD and you would know if it is the equipment or the boat.

I'm really just spit balling trying to help, I don't know much about Garmin units.