It sounds like you've got a diode out in the alternator. An alternator is a 3-phase AC generator, with 6 diodes to rectify the output to DC. One bad diode knocks out the winding it's attached to, plus another one because of the counter-voltage created. The one remaining leg still charges, but at less than 1/3 of rated amperage. it also causes a flicker at low speed.
Jerry