There's a lot of ways a charging system can fail. Keeping the battery charged is only one thing to look at. If a diode fails, "ripple" voltage will be very high and the generator will only be able to develop a maximum of one third of its rated current. With the common 90 amp generator, 30 amps is not enough to run the entire electrical system under all conditions.
To verify the charging system is causing the problem, unplug the three-wire connector while the engine is running and the flickering is occurring. If the flickering stops, be sure all the electrical connections are clean and tight, but the generator is the main suspect.
Tuesday, December 10th, 2013 AT 4:06 PM