I tried to log the slow MySQL queries (by enabling the property in the mysql config file), I waited about one day, and I opened the log file...
The file is about 800KB and contains mostly (about 98% of the file) this query :
# Time: 060302 16:35:41
# User@Host: lelombrik[lelombrik] @ localhost 
# Query_time: 21 Lock_time: 0 Rows_sent: 10 Rows_examined: 1763
SELECT u.id AS userid, t.id, t.subject, t.last_poster, t.last_post_id, t.last_post
FROM punbb_topics AS t
INNER JOIN punbb_forums AS f ON f.id = t.forum_id
LEFT JOIN punbb_forum_perms AS fp ON (fp.forum_id = f.id AND fp.group_id=3)
INNER JOIN punbb_users AS u ON u.username LIKE t.last_poster
WHERE (fp.read_forum IS NULL OR fp.read_forum=1)
ORDER BY t.last_post_id DESC
LIMIT 0, 10;
I didn't look at the PunBB code but I think this should be the index page of the board ?
I don't know why this query is so slow, maybe because of the join with a string... ?
Edit : I tried to rename the extern.php also, but it didn't change anything !