The manuals I downloaded from Xantrex - both installation and owners - have no reference to the warnings you are receiving so the printed manual must be a bit different.
Is the charger wired to the house bank or to both banks?
If you are able in your system try running the fridge off the start battery to see if the same problem occurs. If it works there may be a battery issue - if not the problem lies with the charger. It may eliminate one possibility.
I doubt very much an AC issue - these chargers are very voltage tolerant and it is obviously wired properly.
Living aboard in Victoria Harbour