My charger has 3 stages, Bulk, Absorption and Float. The charger determines the stage by how much current the battery is pulling which is related to how charged the battery is.
Bulk is full voltage and current and stops when the battery is 80% charged.
Absorption is full voltage but limited current and stops when the battery is 95% charged.
Float is limited voltage but full current (potentially) and it stays that way till I recycle it.
In float, the only reason there is hardly any current is because the voltage is just above the battery's voltage and the battery therefore draws hardly any current. However, the charger is still capable of delivering its full current capacity if a load is applied. Thus, when I flush a toilet, the power is coming from the charger, even though it is in float mode. The charger's fan kicks on, because of the current draw, but the charger keeps the voltage at float voltage (which is still a tad above the battery voltage). And the charger never leaves float mode.
Your charger may be different, but it seems that in setting 2, your charger is never entering float mode with all of the batteries connected. It is strange that it did with just one bank connected. As I said above, you can put all the load you want on the charger in float mode. Maybe setting 2 is such that if you had constant loads, it knows this, and delays going to float mode to account for the constant loads, and with the extra batteries it never reached that point.
Also, even if it goes into float mode a little prematurely (the batteries aren't 95% charged), they will still charge because the uncharged voltage will be less than float voltage and current will flow into the batteries until they are charged. But it will be slower than at the other stages where the charger voltage is higher.
This is from my manual ...
If a load is applied during the absorption phase, the charger may revert to the bulk phase depending on the total current draw. When the charger switches to the float phase, it will remain in that phase regardless of current draw. The charger is still able to deliver full output current when in the float phase. To re-initialize the three stage process shut the charger off momentarily, then back on again.