Oh. Yeah. once you toss in a COUNT, it aggregates everything into a single row. The solution would be to add a GROUP BY clause...or actually that will probably not give you the correct row count. You'll either need to use a subquery, or join the table on itself.
This isn't exactly elegant (i'd prefer multiple SQL queries) but...
SELECT username, DATE_FORMAT(join_date, "%d/%m/%y") as join_date_str,
(SELECT COUNT(*) FROM users) AS num_users
ORDER BY join_date
should do it.