Same goes for me, the categories are somehow still there but invisible ..
Found a site about it: http://blog.cumps.be/wordpress-26-upgrade-fix-missing-categories/
but my whole sql database is messed up -_-;;;
so I really don’t know how to fix it..
Try this:
http://ww.wp.xz.cn/extend/plugins/wp-dbmanager/
If it is just the count field in your databse and you have version 2.7 you can try this Query to update your category counts
UPDATE wp_term_taxonomy
SET wp_term_taxonomy.count =
(SELECT count(wp_term_relationships.term_taxonomy_id)
FROM wp_term_relationships, wp_posts
WHERE wp_term_relationships.term_taxonomy_id = wp_term_taxonomy.term_taxonomy_id
AND wp_term_relationships.object_id = wp_posts.ID
AND wp_posts.post_type = ‘post’)
