yup ... it has me stumped. The only thing i can think of is that the isolator was some how letting voltage bleed back so the meter was measuring both batteries.
like i said ... electrical work is wizardry to me ... i just dont understand it all that well.
To get an increase in voltage - as measured at the positive post on the main battery - would require that the auxiliary battery was effectively wired in series with it. That can only be done by the
positive side of one battery (the aux in this case) having a conductive path for current to flow over to the
negative of the other battery (the main). If the positive sides of both batteries were connected, you would not see an increase in voltage - you would only get an increase in current capacity.
It's not something you'd ever see with only a single battery setup. But - with a dual battery system - it is easily explained.
Say the positive cable coming from the auxiliary had a ground fault (IOW not a dead short - because if that were the case, your fusible links would be burning and the underside of your hood would look like the 4th of July - bad medicine) but just a minor leakage of current into the frame. With a single battery system, that would be no different than leaving your dome light on overnight. It would drain the battery down - to some extent.
But things are different with the other battery in the picture. Now, with the 2 batteries, the current flows out of the one battery - the one that has a ground fault into the sheet metal/frame - doesn't all return to the negative post of the "donor" battery. Some percentage of electrons will migrate over to negative post of the 'recipient" battery (i.e. the one that is well insulated from the frame). That is probably what is going on here. And that is why you saw 20 - and not 24 volts at the main's positive.
That is not to say that you don't possibly have an issue with the relay - the short to ground might be in that relay. But as noted above, even if both positive sides connected together, that would not affect the total system voltage or the voltage of either battery. As a matter of fact that is exactly how the circuit works. What is being referred to as an isolation relay is more correctly called a replenishment relay. I am not too articulate today, maybe the description and wiring dwg below will make things more clear.
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The auxiliary battery has no direct connection to the rest of the charging system. It is dependent on the alternator to be recharged - as is the main battery. The difference is, the main and the alternator are always connected and help each other out with carrying the vehicle's electrical load.
The main battery (of any car) only pitches in at the beginning (i.e. when it supplies the power to the starter). After the engine is running, it just sits back and lets the alternator do the bulk of the work. There
are times when demand exceeds the alternator's capacity - like if you are running every electrical component in the truck and playing the radio wicked loud - then the battery has to get off its lazy ass and help out. But that can't last long, because the battery is only a storage device and cannot recharge itself.
Without being there with my Fluke, I can only speculate that the situation described above is accurate. What I would do if it were my truck - and you had no immediate need for the extra battery - would be take it out of the equation and see what happens. To do that is as simple as disconnecting the lead that is bolted to the auxiliary JB and the positive cable from the aux battery positive. The relay itself will still operate - and the contacts will close - but no with no cross connection from the main to the auxiliary, no current will flow.
Then, if things clear up, you can assume there is a problem in the aux positive wiring (read, ground fault). If the main continues to struggle, disconnect it from the main JB. Be sure you disco the load side, not the line side. The rest of the system will still need to be fed with power and that is how it gets it.
If you still have charging problems, disable the relay itself - by yanking the radio fuse - that will cut control power to the coil.
