Well if what are saying is true (and the “isolation/interconnect” relay main contacts are closed and making good contact), then you should see both coach and chassis batteries charging from the converter (identical or close charging voltage on both strings). This would be backwards from the operating description of the IRD document. As you say, it would make you wonder if maybe the ignition sense wire to the IRD was actually connected to the converter feed to the + terminal on the coach battery instead. Since this all worked properly at one time (and no wiring changes made since) then we could “assume” that wiring was and is still correct. I recall seeing recently another poster with an IRD system having a blown fuse in the ignition sense line which was buried inside a taped connection. If that fuse was blown in your situation the ignition sense would not work (so charging from alternator would not close the isolation relay as it should), but that would not explain why when on converter in your current situation, the isolation relay is closing (or staying operated). Possibly the IRD device has itself failed and is just doing strange things?
I have seen some devices on the internet that can be purchased to change an IRD to operate like a BIRD (to enable true bidirectional battery charging), but can’t advise you which way to go. I am lucky to have an old ACE with a BCC and the electronics which allows for bi-directional battery charging. If your IRD unit has failed then maybe it would be worth checking out the alternatives for bi-directional control.
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