Yes your batteries are more than likely the root cause for this problem. How old are the batteries? Also make sure that when the boat is in storage that the battery switch is turned to the off position. Also make sure that the amp is wired to the battery switch. Amplifiers & stereos have a constant draw for the preset memories( radio stations & such). If the amp or stereo is not wired through the battery switch they can draw down the battery over time leaving you with a battery that is not fully charged. If the batteries are over 4-5 years old it is recommended to replace with new. For carbuerated motors use a deep cycle battery. For fuel injected motors you will need to run a cranking battery. I have always had great success with Interstate batteries for my customers.

Walker Marine