why is my puppy’s hair thinning?

2 weeks ago I took a puppy home. Friends found her and her brother abandoned. She checked out great on her 1st vet-trip, but recently her hair has been getting really thin – mostly around her ears and inside her legs, but all over. Today the vet did a “skin scrape” to check her for mites etc. and she is mite/mange free. She is very happy, energetic, and affectionate.
I’ve been feeding her eukanuba dry puppy food mixed with canned Merrick or Wellness for puppies.
I don’t know what breed x she is, but she is black/tan like a dobie, with long legs/small frame. She is 10lbs at approx 10weeks and the vet guesses will be abt 30lbs grown. The hair around her ears is wavy like a spaniel and the rest of her coat fluffy/course.
She does have some fleas tho we treated her with frontline, sprayed the yard, put DE around house. Vet said she may have had a reaction to FL so switched to Corvis and prescribed Relief shampoo. Any ideas? Pics at: http://www.flickr.com/photos/27810004@N07/