Try to think from a Pavlovian standpoint, if you are getting the snake out of the cage for both feeding and handling then how is the animal to know the difference until you get to the feeding enclosure? That little window is were your trouble is most likely to occur in my experience. Feeding in the cage means you do not have to move the animal after feeding, and the specimen understands that being picked up is not a time for feeding.
I feed in the enclosure, and am actually adding "trap doors" for my larger constrictors in order to further reinforce a dichotomy between chow time and play time. The trap doors will only be used for distributing prey.