Check the voltage at the battery with the engine running at about 2000rpm and nothing turned on. You can use the control box to adjust the voltage to be between 13.7v (if you drive the car on the freeway a lot), and 14.4v (if you mostly city drive the car). If it is already reading between those voltages, then you may have a weak connection at the generator, solenoid or control box.
Also, check that the battery voltage is at least 12.6v while sitting and engine not running. A cell can go bad and suck amperage from the generator.