I've had that problem, started with a bad stator found after the bike wouldn't start.
After changing the stator and rectifier with aftermarket parts, about 5,000 miles later I kept burning out headlamps.
Found out the rectifier was pumping out 18V!
Changed the rectifier, all was well for about 2 weeks, then intermittant headlights.
Rectifier ok, stator ok, battery charging normally, fuses ok.
Changed the relay package.......then the low didn't work at all.
Changed the starter relay.......everything works.
Funny thing is, this morning driving to work..........no low beam (10,000 miles since the starter magnetic switch replacement), I'm hoping its just normal bulb burnout!!!