I may be coming out of no where but I think this is a pain issue. Either he is in pain or thinks he is in pain still from his injury, so there fore he does not want to run. He associates the alley way with pain and having to run so he does not want to go in.
My suggestion is to get him checked up to see if he is okay and if he is, use him as a trail horse for a while or something different to let him realize that he is going to be fine.
This may not be the best advice but it's something to build on.