I'm wondering if you charge the cranking battery when you put the boat in the garage after a day on the lake. Your motor may not be fully charging it just by driving it around, so you may NOT be starting the day off with a fully-charged battery.

My cranking battery used to be fully re-charged by the motor when I just had one 5" B&W fish finder, but now with two fairly large color/GPS units it's not enough, even with lots of trolling around. So I bought an extra charger just to do the cranking battery... no more problems.