I recommend an isolation switch at the battery. if you are draining the battery while it is on the trailer that will solve that problem. If you only have the problem after it has besetting for a few days I don't think it would be the alternator but I could be wrong. My boat has a run/auto switch for the bilge pump. I never turn it to auto unless it is in an open slip and expecting heavy rain. I learned that lesson the hard way..