I'm pretty sure it '''is''' flash, Shane. Just because taking out your battery changed the situation doesn't mean that flash is not the cause. I would suspect that the fans don't kick in when you don't have the battery in because:
# the battery produces heat
# the place where the battery should be may allow for more cooling and ventilation.
If you want to keep this from happening, maybe you should check out [http://clicktoflash.com/|Click to Flash], which blocks flash unless you say otherwise. This may help preserve your battery life as well.