Would seam your entire database is compromised somehow. You mentioned encountering problems, how did you restore? Did you restore just the files and not the database? Only thing I can suggest is starting all over with a fresh install or trying to repair the issues manually; running CB tools and clicking the fix links will do what they can, but make a backup before doing so! Also please upgrade to CB 1.4 and ensure on Joomla 1.5.22 for most stable and secure install.