My Swedish is awful , so I am writing in English. I just moved from ZG, and, firstly, I can tell you that Zagreb is full of people from B-H, so you shouldn't have any problems. Many of my colleagues were from B-H, I have never heard that anyone had any more problems than standard mocking for the accent which you get if you are from any other part of Croatia too.
Also, I saw many concerts performed by Serbian bands (like pop-rock), and I don't think any of them had experienced some problems. (Maybe if you would specially provoke with three-finger-salute - but otherwise, really, no.)