Yes, That's definitely a problem if batteries are in parallel without any isolator - they will drain each other - even if the batteries are of the same quality they will drain each other like a yoyo..
I only use the "all" or "both" position when charging up on longer trips, and when starting up after long periods of storage.

I always run a single battery at a time when on anchor and running equipment.. or when running back after I exhausted one hanging on the line..