It sounds like your thruster battery is somehow possibly paralleled with the engine start battery. I don't think it would be possible the way my R25 is wired. First visually check your cables and switches. My switches are all on/off switches but there is an emergency parallel switch for when the engine start battery is low. Check that the parallel switch is off. The grounds of all your batteries will be connected together, but make sure the thruster positive battery cable is not paralleled with anything else.
I believe you are absolutely correct, as delivered from the factory. This, however, is the 2011 boat and I do not think the first owner. Several owners have wired their thruster battery in parallel with the house batteries in order to provide more capacity when at anchor. I have actually done this though I had a switch installed so that I can isolate until I am actually anchored out. I then disconnect before leaving the anchorage/mooring putting things back to the factory set up. Even without the separate switch, there is normally no threat to the engine battery since the ACR will isolate in times of a heavy voltage drop with the windlass. [I'm assuming ACR's were installed in 2011 as standard equipment]. As you pointed out, if the parallel switch is turned on then the ACR's are irrelevant. I agree that the first step is to check that the parallel switch is off. Hope this helps.