I have this same problem with my house batteries overcharging, and my engine battery not whenever the engine rpms are above idle. I noticed the problem after my inverter (Heart Interface 2500) started shutting down from an over-voltage condition when we were underway, and the a/c outlets stopped working.
I've checked the voltages at the batteries with the hi-idle on and the engine batteries were at 14.4 and the house batteries were at 16.2 upon arriving home after a trip (all fully charged). I removed all the batteries from the coach, and removed all the wires from the isolator terminals. I checked the isolator, a Powerline 190 amp, with a multimeter that has the diode check function. With the meter positive on the center terminal, the forward biased voltage drops were 0.453v and 0.481, and with the meter negative on the center terminal, the reverse bias was infinity, so the isolator checks good with this test.
However, I wanted to test the isolator when it was carrying a charge current, so I split my house batteries into 2 banks, with a common negative, and the positives run with some identical 10 ft. 2 ga cables with ring terminals to the outboard terminals on the isolator. I attached a separate 2 ft. 2 ga cable with a ring terminal on one end and a lead post terminal on the other end to the center terminal of the isolator. I tightened all the connections, and hooked my big portable charger/booster up to charge the 2 banks thru the isolator; each thru a separate diode bank of the isolator.
Both battery banks (6v golfcart) were at 12.88 volts to start. There was an immediate difference in applied voltage between each bank, and it increased as I went from low to medium to high to start on the charger charge settings. I measured the voltage drops across the 2 diode banks, and they were 3.2v and 2.2 volts when on high.
There is at least 1 volt difference in the voltage drops across the diode banks, so to assume that whatever the alternator is putting out is applied equally to both banks is incorrect. My isolator works, but probably has a problem (as the original poster was thinking).
The link above to the Hehr website doesn't work from my iPhone. The server cannot be found. I'd like to troubleshoot the isolator before I buy a new one, or get something better, since the price is the same.