I've run into a handful of systems with this issue since we migrated to our new CM2012 server. Some clients still have the old server's site code, no matter how we install the new client. The site code value can be found in the registry, and removing the value and installing the new client did the trick for us.
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\SMS\Mobile Client\
Source: http://myitforum.com/myitforumwp/2012/10/05/configmgr-client-gpo-assignment-removal/
