Alas this is a long dead thread - long before my time.
Alas the solution is to reduce the inter-battery resistance. Isolators should only add milli-Ohms to the interconnection.
For the OP and other suggestors, and readers - the alternator does not stop charging, it continues to put out its 13.8V to 14.4V set voltage. The main battery merely stops absorbing current (except for its "float" current - typically up to an Amp or two).
The other batteries are still being supplied with that same (say) 14.2V, but their is voltage drop along the distribution because if the IR losses (current I through the interconnection resistance R, where the current I is the sum of the battery's recharge current plus its load current.
It is not a mere case if averaging or sampling voltages - that is inappropriate without some form of regulator between the alternator and the "higher voltage" battery(s) (eg - a PWM chopper).
Summary: Improve your inter-battery distribution. Ensure there are minimal voltage drops to the battery +12V and along the ground path.
PS - Simbalage, do you have a charge light?