You probably have a left over term with the same name of your category in the terms table
What happen is that the plugin check if the category exist if dosn’t exist it will try to create it but if find a term with the same name will create a new one with the same name and an consecutive sufix.
Try to see witch are the categories with problems and have a look at the Terms table.
this query can be useful to know the used taxonomies
SELECT t.term_id, count(tr.object_id) AS times_used, t.name, t.slug, tt.term_taxonomy_id, tt.taxonomy, tr.object_id
FROM wp_terms t
LEFT JOIN wp_term_taxonomy tt USING (term_id)
LEFT JOIN wp_term_relationships tr USING (term_taxonomy_id)
GROUP BY t.term_id
HAVING tt.taxonomy = "your taxonomy"
ORDER BY times_used desc wp_articles
hope that helps,
I used this plugin for 100000 post and work fine took me about 3 hours.
