[puddleglum]

Do you have a way to load test your batteries individually and/or test the voltage of each battery while it is under load in the car? If you are using used batteries, even if the batteries all show fully charged, they may be way different under load, as mechman said. You should make sure your batteries are good before looking further IMO. If there is a current cutback setting in the controller, it may be shutting you down if the battery voltage is falling to low.