If you have recently run a scan with Privacy Controls, it is possible your Firefox bookmarks were removed.
 

This is because Firefox stores bookmark data in a single location that is also used to store information about your browsing history. When your browsing history is removed you may also lose bookmark information.

 Please visit the link here for more information on how to restore any lost bookmark privileges.

To prevent Privacy Controls from removing this information in the future:

 

  1. Please open Privacy Controls and go to Options along the left hand side.
  2. Select the More Info button along the right hand side, next to the internet browsing history section.
  3. Expand the category that corresponds to Firefox by clicking the + (plus sign) besides "Firefox".
  4. Now deselect Browsing History, along with any other categories you do not wish to have cleaned.
     

After making the changes above, Privacy Controls will no longer remove your Firefox bookmarks during a scan.