A friend of mine got a problem with his newly upgrade WordPress (2.6.2) that is missing categories. The problem occured randomly. If the categories showed correctly and then he clicked it, there was no post assosiated (404 Not Found).
You just need to run this query:
UPDATE wp_term_taxonomy,wp_terms SET wp_term_taxonomy.description = wp_terms.name WHERE wp_term_taxonomy.term_id = wp_terms.term_id
You may also check other solutions if the solution above is not working.