Boondocker is a poor choice most boondocking. As soon as it hits 14.6 volts(at the converter) the Boondocker drops to 13.6 trickle mode. This might be OK with a 35 amp into 4 batteries and mounted close. But 55+ amps, 20' of wire away from 2 batteries will act just as you describe.
Progressive Dynamics or IOTA is a much better choice as the higher voltage is held 4+ hours and you get a decent charge into the battery.
Your best shot is to run the generator in the morning to do some heavy lifting and then let the solar take over once Boondocker drops to 13.6 volts.