I had a similar problem and it ended up being a bad transfer switch (the one making the thunk sound. They don't have a great life span. I went through blaming the power source, the surge guard and it was fixed when the switch got repla ed. Good luck
I have a 2013 CRV toad and only go through the set up if I stop for a couple of hours. Been towing it for a couple of years and not had a problem. My CRV has the full electronic package with GPS. I found the battery goes dead after a few hours if the fuse is not disconnected. I purchased a fuse switch on line and it has solved the problem ( as long as I don't forget to turn it off). Good luck!