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I am guessing that the house batteries are wired wrong OR a lead was left off. That is the most obvious probable cause. This happens frequently and it seems to be done by people who should know better. Look for either a lead that was left off OR is a positive red lead on the negative side of one of the batteries. Attach a photo of the tops and cables and perhaps I can spot the problem. All follow ups are included in our fee.
A shortstop breaker to those may be tripped. Hard to imagine that these items BEFORE you changed out the batteries and that now they don't. They pretty much had to do something here and IF they work with the AUX start which connects the batteries together then it has to be something there. Always possible that one of the batteries is defective. We see this frequently. Just because it is new doesn't mean that it is going to be good. If you don't find any other cause I would have them load tested and find out. Most places that sell batteries can do this for you. Surface voltage means nothing really.
No........and if they work with the engine running then there is nothing wrong with the circuit EXCEPT from the batteries you had changed. I will opt out of this and let another tech offer something if they have another idea.