I had a weak battery and the indicators would light up, but they wouldn't flash. Don't know how old your battery is or whether you should check the specific gravity. Doesn't explain why the rear indicators would work and not the front though does it? Have you checked the fuses? Not sure if this will help as I don't know the relay you have, but it might be worth a read http://www.ehow.co.uk/how_7789429_test-threeprong-flasher-relay.html.
Found this helpful for explaining how the circuit works http://www.yamaha-triples.org/workshop/harnett-signals.asp. Might be of some use too. ??
I'm sure someone here will have a better idea. Might want to list all the steps you've taken so far.