I think I am also experinecing a similar situtation with my new puppy. My puppy is 14 weeks old, and we only been having him for 5 days, which 3 of them, my girlfriend was with him only. He has bonded with girlfriend not leaving her side or letting her out of his site.
As I returned from my trip I was ancious to play with my new puppy, but I was greeted with a grouled instead. His behaviore is quite fearful of me, he runs away as I am trying to pet him.
The little reserch I have done so far, the words submissive urination and socialization have been coming up.
I'll let you know if I find any solid answers or fixes, please do the same for me.