A 20A breaker seemed kind of low to me so I checked the installation
manual on the Xantrex website for a Freedom 3000. It says the max breaker size for the AC Input is 30A. I did see on the spec sheet that it is rated for 22A AC input. So I would change the 20A breaker to 30A if it were my boat
. If you have have clamp-on ammeter you could put that on the hot out of the breaker and see what amps it is drawing when the batteries are low.
Other than that you should check the entire AC side wiring
and look for loose connections, good terminals, and proper wire size (10ga min). A loose wire on the breaker could make it pop every time.
The F3000 should not have any problem charging your batteries, and it is internally protected as well.