I recently wrote a post that discussed how the contributor rights had been stripped off areas in TFS 2012 server when QU1 was applied, this included details on the patches to apply the manual steps to resolve the problem.
Well today I found that it is not just in the area security you can see this problem. We found it too in the main source code repository. Again the [Team project]\contributors group was completely missing. I had to re-add it manually. Once this was done all was OK for the users
FYI: You might ask how I missed this before, most of the users on this project had higher levels of rights granted by being members of other groups. It was not until someone was re-assigned between team we noticed.