could it be simply running low on fuel? I dont know anything about this bike BTW, hopefully someone who knows them will chime in. Perhaps there is two fuel tanks, a main and a reserve ? Have you studied the owner manual? I take it you bought it private sale
If you havent got a user manual, download one for free here, just select the year
http://www.yamaha-motor.eu/uk/services/owner-manuals/index.aspx