My National Luna dual battery setup ( the solenoid with the timer function), always favours the main battery to be charged, first.
So, when driving, the solenoid timer will allow the main battery to be charged for 10-15 minutes first , then only switch to charging the auxiliary battery.
With the solar charging option, only the auxiliary battery is charged.
No option function for the main battery to charge too.
I have an override option to use the auxiliary battery to start the vehicle, should the main battery prove too flat, but you have max 2 tries from the auxiliary battery.
It also shortens the deepcycle's lifetime , doing the heavy discharge needed to power a starter motor.
The theory is that the main battery should never charge to auxiliary, and vice versa.
Alternator charge mains for a set period, then the auxiliary.
Additional solar is for the auxiliary only , unless connected as you describe, in an emergency.
What you describe, unless specifically installed or designed as such, does not sound correct.
Edit: My conclusion is either your main battery is showing signs of end of live or your setup is incorrect.
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