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Brian,
The best way to work on this problem is to understand it better. The routine that you are describing at the food bowl may be a good way to “test” for an initial problem with food guarding, but a VERY bad way to prevent food guarding. What you are actually doing is teaching her there is a reason to guard her food. Think of it from the dog’s point of view. She is a rescue so she probably came from an environment where she competed for food with her littermates – so only dealt with competition at the bowl. Probably she never encountered any person messing with her when she ate so didn’t have much of a problem with people. Suddenly, she is in a situation where whenever she eats there is a hand blocking her food and hands basically annoying her. Dogs don’t do that to each other, we don’t do that to eachother (or even expect to do that to our children), so doesn’t make sense to do that to them. I’ve seen a lot of dogs learn to become more anxious and aggressive around their food because of this and it has nothing to do with alpha stuff or pecking order. If you do anything around her food it should be to teach her it is a GOOD thing when people approach – especially children and maybe throw something even better into her bowl while she is eating and then just leave her be. If for some reason we need to call her away from a bowl or take food away she isn’t supposed to have we incorporate formal obedience.
An equivalent example would be if everytime she took a nap on her dog bed you came over and started pulling her tail – then had your son do that. You would actually train her to become more defensive when she rests. We the humans must be the ones that she looks toward for guidance and protection when she is eating. When she is done eating we take away what she doesn’t finish – so there is nothing for her to worry about.
Watch these two videos – it may give a little more insight:
http://www.youtube.com/watch?v=3n1R0lXTgJ0
and this one:
http://www.youtube.com/watch?v=owjyJh2NlfE
