Make sure that your new flasher relay is a variable load. It'll say that on the package. If this is a Yamaha with self cancelling signals you will probably lose that function. On my yamaha sr500 I had to reverse the polarity on one side of the bike by plugging the black wire, usually the ground, into the power and the red wire, the power side, into the ground from the harness while leaving the other side plugged correctly. That cured my problem and every thing worked fine.
Terry
J'ville, Fl.