This information is for the 1100 Evo but I'm guessing it will also apply to your 1100S.
There are a couple of relays under the tank and they can work loose causing intermittent problems. (My injector relay popped out just enough to break contact and now it's held on with a cable tie for security.)
Have you checked your error log? If the relay is causing problems, you may see the message "LIGHT". Note that, if the problem is intermittent then the error message might not be there as it will probably reset when the light starts working again.
On the Evo, the relay is under the tank by the ECU, so easily disturbed when removing the ECU. Make sure it's pushed fully home.
Before you go to the trouble of removing the tank, also look at the headlight connector on the steering stem - they can become loose/corroded causing the problems you describe.
