It could be either. Some children are Lactose intolerant so the milk may cause more runny poop once the milk is in the system for a while, and other kids show symptoms instantly. On the other hand, one side effect of the shots can be diarrhea. I'd probably take her off the milk for just a little bit and see if it clears up. Then, in a week or 2, providing it clears up, do another experiment by adding the milk again and see if it comes back. If it comes back, then you know it's the milk. In the meantime, you could do a soy milk. (I'm not a soy drinker myself and prefer milk, so I'd suggest the Vanilla flavored one as a good substitute.) If it doesn't come back, then you'll know that the runny poop was probably just a side effect of the boosters. If nothing stops it...I'd get her in to the Dr.