Updated 6th Nov 2013 - Also see this updated post , the API mentioned here maybe an issue, but the rights change in this other post is probably the real issue
After upgrading a test server from TFS 2012 to 2013 I started getting the following exception when trying to set the retention for a build policy via the TFS API
"TF215106: Access denied. TYPHOONTFS\\TFSService needs Update build information permissions for build definition ClassLibrary1.Main.Manual in team project Scrum to perform the action. For more information, contact the Team Foundation Server administrator."}
This was a surprising error, the code had been working OK and the TFSService account is, well the service account, so has full rights.
The issue was I also needed to rebuild my application with the TFS 2013 API, once I rebuild with the 2013 DLLs it all worked fine.