are you trying run the inverter to keep the "commercial" refrigerator running?... if so, depending on the converter you have, there may not be enough power left to let the converter charge the batteries.
the honda2000 only delivers about 15amps @ 120vac... a commercial fridge can use 15amps AC or more, and running it thru an inverter, it will consume a substantial amount more... if its not being ran thru the inverter, it STILL could be taking all the power being produced by the generator.
unplug the fridge and see if you get the right charge output from the charger to the batteries, without it in the circuits...