If the pup is cowering down at only 13 weeks old then it either has a naturally very submissive and nervous temperament, or you've already given her reason to be afraid of you: which is it?
You say: I do make a fuss of it and praise her but sometimes it's hard when it's throwing it down: so does that mean you have got cross with her, grabbed her as she's trying to run off? If you have mistakenly hurt her by doing that, and the pup is also very sensitive, then you have your answer. The thing you need most with pups is endless patience, and then some more patience. Pups are naturally hard wir