Sounds like either you're drawing too much current in the brake light system or your alternator is not charging the battery fully.
On the brake light system, have you added additional lights or changed the type of bulbs in the lights. If so, you may have exceed the output of your charging system. I've seen people put so many lights on the back of their bikes that they've burned up alternator stators on a regular basis.
To check your charging system, put a battery charger on your battery and bring it to full charge. Then connect a digital multimeter to your battery, red lead to positive, black to negative, 50 volt scale. Start the engine and bring the idle speed up just a bit. After about a minute or so, the meter should read about 14.5 volts to 15.5 volts. Any higher or lower could indicate problems. If you find this, repost with that problem and I'll tell you how to check the alternator with your meter.
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