I’ve had some customers that are experiencing this issue so wanted to get it out more broadly in case you are having similar problems.  Buck Hodges has written a blog post on symptoms and resolution here:

http://blogs.msdn.com/b/visualstudioalm/archive/2012/12/21/tfs-2012-update-1-permissions-lost-on-attaching-a-collection-fix-available-in-early-january.aspx

The KB article can be found here:

http://support.microsoft.com/kb/2803625

There are several other issues fixed with this TFS Update.  Here is the list of issues that are fixed (for more detail go to the KB article):

Issue 1: Collections that are attached to a server that is running TFS 2012 Update 1 may lose permissions

Issue 2: Group scopes may incorrectly cause permission errors

Issue 3: Severe decrease in performance after TFS 2012 Update 1 is installed

Issue 4: Identity sync jobs may fail repeatedly

Issue 5: Warehouse is not updated correctly, or fields that represent a person are not filled

Issue 6: Users can see names of collections of which they are not a member

Issue 7: You cannot remove a user or a group after you attach a collection to a TFS 2012 Update 1 server

Issue 8: You cannot view artifacts that reference an identity that is no longer a part of a collection