Any ideas on why my shoulder is hurting? Its the one I carry backpack on.

It's the backpack. Back/shoulder problems are very common in people that carry backpacks. The problem likelihood increases dramatically if you are using only one shoulder. Use both shoulders, make sure is well-placed in the middle of your back, and don't make it too heavy. Make sure it is tightly closed, and snug on you, preventing the brute that wants to steel your ipad.