You take-off both the posiitive and negative from Battery (Bank) 1? You should, in my opinion, other wise you're not going to be charging that battery back.

Unless something changed, you MUST not every attempt to run the Heart (Xantrex) Freedom Charger without a battery connected to it. If you do this, you'll FRY your Charger (and Inverter) board(s). Because of that, you have done properly IF you connect the battery directly to the Alternator without a switch. (

That's one reason that you have to be VERY CAREFUL whenever an inverter is around that the AC circuits might be HOT even though you don't notice it. You have to disconnect the alternator from the AC circuits or else you can get someone killed because you don't realize that the alternator is on standby and it looks like the AC is not "live" with the shorepower 'off', but the Inverter kicks in and kills someone.

Anyway, if you have a combiner, or you simply then put the batteries on "both" you should be charging Battery (Banks) 1 and 2.

If you're monitoring both battery banks, you should have the leads sent to both Batteries, measuring both the hot and neutrals. The "shunt" should seperate them.

You have the manuals for the Line 2000 and the Xantrex? Are they connected as suggested in the manuals?