Time machine file restore fails "you don't have permissions to access.."

Frequently I work my macbook (10.7.3) in the terminal as root.  I seems like files that owned by root are not eligable for restore via time machine by the system administrator.   Is there a way to operate time machine as root?   Or is there a way to grant root rights to the user account designated as administrator?
Specifically, the time machine copy dialog reports "The operation can't be completed because you don't have permission to access [filename].   For example, in one case case, it is .gitignore.

In post https://discussions.apple.com/message/9945786#9945786 Scott T. states that "time machine always runs as root.", I take that to mean that time machine will have rights to copy all files, regardless of the owner. 
That's great.  So I can restate the question: how do I restore a file that is owned by root?

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    It seems that the critical folders have the same permissions. Where else should I look?
    Message was edited by: Hugacrv

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