Rich, all the important info is missing. I suggest going through Shane Ross's tutorials on tapeless workflow and offline/online workflow to check that you are following the best procedure. How you backed up your file structure and captured the media to ProRes proxy are the important first steps before you go through the media manager stage and how you setup MM also matters.
http://library.creativecow.net/search.php?q=shane+ross+tapeless+tutorial&f[...