VSR detects when the charging voltage at the start bat is above a certain level (~13v from memory)and then couples both batteries to the charging source so the House batt gets charged. When you turn off the engine or charger the VSr disconnects the House batt from the start batt so the House systems can not discharge your start batt. It does not automatically parallel the batteries like you suggest. That is why you have the Emg Parallel switch, You probably have a bad batt, but it could also be a bad cable connection so check those first. Simple test would be to swap the two batteries around and see if the problem stays or goes away.

Hi again, on a related matter, my mate has the same battery setup on his boat as mine, and he was out boating last weekend and the little red charging light on his VSR never lit up. Presumably this would indicate the second battery never received a boost, and batt 1's voltage never exceeded 13.4v? Would that be right? Batt 1 is brand new.

Yep your start battery is stuffed, and 5 years is a particularly good life for it. Your mates battery is not charging to trigger the VSR to charge the other battery, so it may be stuffed as well. Or you have something more serious like the regulator has gone bad on your engine too.

If your battery is five years old why not say "thanks for the service" and buy a new one? Without a good battery all that equipment worth thousands of dollars might not do a damn thing!