It's always worth going over all the electrical connectors to make sure they're clean and making good contact, but I agree with everyone's opinion that sub-3000rpm engine speeds are too low to charge the battery when the headlights are on.
As an alternative to a lower gear, you could consider fitting LED riding lights if you're just using the headlights to be seen rather than to see by. They are intense enough to make sure you get noticed and only draw a fraction of the current that a quartz-halogen bulb takes, wire them to the sidelight circuit or use a separate switch and the load on the battery will be reduced by about 9 amps.