Sounds like your relay/isolator is working. I would check for charging voltage on either side of the isolator. Mine has 2, one for the chassis battery and one for the house batteries. If you see 13.7 + volts on both sides of the isolator then your relay is good. I would then try to trace the + wire to your house batteries if there is no corrosion then I would assume as others have said, someone did not tighten or installed incorrectly the wires they were meant for the fix. I assumed that you put a voltmeter across the + and - of the battery terminal while it was running and read something less than 12.7 volts?