Are you saying that with the battery in the bike, but not connected although fully charged you get about 12. 4 volts (on a digital volt meter) then when you connect up it gives 9 volts? If so, that is a mighty discharge and you would see the terminal 'flash' as you connected the battery (ie a short to earth/frame) somewhere.
A bit more info required. Year of bike. Battery age. ES model or kicker only etc etc Might just be a duff battery but
??