if you run two batteries ,they constantly charge and discharge till they both go dead.
so this relay only connects the second battery when the ignition is on.
that shoukl help.
FYI - It's very common to run two batteries in off-road vehicles. They typically run a small starter battery and a big deep cell like a large yellow top or odyssey for the winch. No discharge issues as you described. I can source a write up if you need one. Check expeditionportal.com.
In general, yellow tops aren't the best starter batteries.