Just the other day I noticed my lights flickering as well, both at idle and increased rpm. This stumped me for a second because the battery never gave me a starting issue even after sitting a couple of weeks at a time and not being on a charger. What gave it away was the tach. It started acting crazy, then the idle would fluctuate badly for split seconds at a time. My first check was the battery terminals. Hand check-tight nothing moved, get the screwdriver-positive battery terminal still had about 1/8 turn left- problem solved. The battery was then put back on a charger.
Batteries have been know to do weird things to the bike. The fact that you had to jump it says there is something going on with the battery. One thing that people fail to realize sometimes is a battery can have 12 volts, turn on the lights, beep the horn and still will not crank the bike because the amps are too low. A battery may even start the bike but may not receive a sufficient charge from the bikes charging system if the battery has a bad cell.
Granted your issue may be something else electrical related, but I would look at the wiki to see what else could mimic the symptoms you describe.
http://www.ninjette.org/wiki/Battery