You don't mention what boat you have but if it is like mine, a 46 Bertram, I don't have separate engine and service battery banks. Each engine has its own batteries and the various electrical components have been connected via panels that have two groups of circuit breakers fed by each battery group. There have been times when the surge required for starting engines has brought the voltage down enough to have what you are experiencing but mainly with my radar. I also had problems with electric fishing rods fed by 24V to 12V converters that are extremely sensitive (electronics) and would have quite a bit of problems when starting a retrieve and just stop working. My installer correctly identified the problem as a surge creating enough voltage drop to create these types of problems with sensitive electronic circuits. Changed to much thicker wires and still had problems but totally solved by installing condensers in the line to compensate for the momentary drop. Might be a solution also for sensitive electronics in your case. Maybe the more technical folk here can comment if this makes any sense. Sometimes, when engines are cold and your batteries are a little tired the problem can be more frequent. I also replaced all my batteries, chargers and converters but the the only thing that solved the electric reel problem were the condensers.
Rolando