The rear brake switch harness looks pretty long, so maybe the connection is high up under the seat?
http://www.cscmotorcycles.com/The-br...-p/z49-101.htm
Follow it up from the switch and make sure the connector is secure. If so, then disconnect and inspect that the metal connections are fully seated in their holes. If they are, then test the switch with a meter.
Good luck, let us know what you find.
I'd go to the garage to look at mine to give better advice, but it's late, cold and I'm in my pajamas. One on each foot.