Gary,
The isolator can not cause batteries to over charge. The terminal labeled A alt, comes from the alternator. It feeds the output terminal through two large high current diodes, one going to terminal 1 for main battery, and 2 for the second battery bank. The diodes prevent current from going in the reverse direction from one battery bank to the other. (Isolator)
With the engine running, measure from the alt pin to ground, and you should see about 13.8 to 14.4 volts or so, if your batteries are charged and in good shape. At terminal two or three to ground, you should see several tenths of a volt lower than the A terminal, which is caused by the diode voltage drop. You can take this measurement at the battery + terminals.
My guess is that, you either have a voltage regulation issue, from either the alternator or charger. Check what voltage you are seeing at the batteries. It typically should be 14V or less while charging. If that is normal, you probably have a bad cell in a battery. A shorted cell will boil off, and draw a lot of current. This is a likely cause of what you are seeing. A battery load tester should be used individually on each battery, while they are disconnected from the coach and other batteries in the bank. Hope this helps.
later Ed
