Trib,
Are you trying to use Bluetooth to communicate with the bike, or to the Arduino board on the bike?
When the bike is off, the OBD voltage is +-12volts. When the bike is running you will get some switching spikes and alternator noise that would show up on an Oscope. Your circuit may need some capactors or more shielding.
I can log my Suzuki with my laptop while riding on the road with no problems. I still need to finish my Arduino however.