Mine does this too sometimes, especially if you rev the engine during the warm up period. The owners manual says it will blink to indicate that the speed sensor circuit needs to be looked at by a Yamaha dealer. I figured the revving of the engine maybe fools the computer to think the quad is moving and it isnt regisitering any speed? In any rate, I just shut it off and restart the quad and it seems to be fine. I have never had a problem with it and I just let it warm up now before I try to ride and or/rev the engine at all and I never get it anymore.
Now that I adjusted the valves, the quad starts right up and idles great with the choke so I dont have to manually hold the throttle in anymore and it doesnt happen unless I try to move it cold.
Jim