I would have looked in the dog food.
AV,Interesting that you mention that, because our dog has been sick on and off almost since we got her (bloody stool, but the vet can't figure out why). Each time we switch foods she seems to get better for a few days, but then it comes back (and we're giving her the expensive "prescription" stuff). I'm beginning to think it might be worth the effort to trace the origins of *all* of this dog food and see if there's a common source for one or more of the ingredients...
Oh poor little thing! There was a helluva uproar here a while back over the dog food - a number of dogs actually died - and of course, ingredients were traced back to China. Funny thing with those prescription dog foods, sometimes they're not everything they're cracked up to be. You might consider just cooking for her and see how she does. My one old dog always had gut woes and I eventually just cooked for him - so long as you cook a balanced meal, she'll get all the nutrients. Chicken, veggies and rice are a good mix - and chicken and rice is also very gentle on doggy digestive systems. Give her a snuggle from me.
AV,Actually, what you suggest has crossed my mind, and if her problems continue I think it's a reasonable course of action. She was the last puppy taken from the litter, so it's probably safe to assume that she was the "runt" (she's undersized for her age, etc.), but hopefully we can get her healthy and happy.