I just went thru a similar situation on my '07 RKC. But mine only lasted about 3 times before it totally died, so you're luck in that way.
I have the "no button" keyfob, and the HFSSM (hands free security system module). Don't know if that was available on your bike, but maybe something similar. My bike did the same thing, went to start it (not actually started) and the flashers went off 3 times or so. I thought that was kinda strange, and I had n different fob close by, so swaped and off I went. When I went to start it again, the bike thought I was trying to steal it. Nothing. Replaced the fob battery, no go. Turned out to be the module needed replaceing. Dealer has to reprogram the new module to your fobs.
Got mine done as a "goodwill" warranty item from HD of Palm Beach, Fl.