Larry, that sounds very similar to what my system was doing before installing a 3rd battery. The only difference is the shutting off of the batteries for 30 seconds to reset the system. I didn't have to do that. The flickering comes when the voltage drop is getting close the the minimum required for the C80...its just reaching that 11volt area and starts to phase out like that...similar to a flashlight with a battery running low, except you don't want to smack it!....if you put it in gear and run with some speed, the alternator on the engine keeps up with demand, but when you slow back down, a weak or undercharged battery becomes a problem again.
The system needs a full charged battery set up so if you leave the dock topped off you should be OK, other than when you turn over the starters, which is really no big deal. But with all the stuff on a boat these days, chartplotter, radar, FM stereo, laptops etc this may put more of a drain on the battery, so I installed a solar panel and 3rd box. I ran a back up +/- cable between #3 and the other batteries "just in case" I need power to the electronics, or a spare start for the engines, but otherwise they are isolated. I think the newer/bigger GW's have a better overall system which eliminates this issue, but the older smaller boats may run into this.