The light flickering means that the alternator is putting out just enough to keep the light from tripping. My lights on my 1009 stay on immediately after startup until I rev the engine. They stay off from then on.
As was stated, check your belt tension. Some belt 'flap' while idling is ok, but if it's excessive, try tightening them a little more.
What is the voltmeter doing while the lights are on? Is it solidly in the green or is it closer to the yellow?
If you can get a digital volt meter/multimeter, check the voltage at the batteries with it idling while the light is flickering. You'll probably find that it's somewhere in the mid 13V range.
The light staying on means there's a problem with the alternator, not that the alternator is working. The problem could be as small as the voltage sensing wire on the back of the alternator is not making a good connection to as large as the alternator has failed.
Later,
Joe