Mine does the same thing. My problem is the ground on the Neutral Safety Switch that allows me to run the starter when the bike is in neutral is loose. You can either pull the covers off and find this and reground it, trace it on the wiring diagram and snip and ground it (allowing you to press start when the bike is in gear) or my personal favorite hook the starter up to a lead and a switch.

I use an alligator clip for mine, so that I can take it off after the bike is started and tuck it back inside under the seat where it sits snug in it's little red plastic sleeve. Except for it bouncing around with every bump, it's never caused a short or other problem (I put a safety fuse inline, too).