I haven't mention the update because i'm not sure if the problem occured after the latest update. I had until now only one client, one ftp user and one shell user and i have performed all the updates since the initial install of ispconfig 3.0 (the client and the users were created just after the initial install).
grep sshusers /etc/group returns nothing.
Regarding the ftp users, when i edit the problematic new user and change his password, i can see with phpmyadmin that his password is changing in the ispconfig's database (although is encrypted but i can see characters changing). Pure-ftpd continues to report that the password is wrong. It seems like pure-ftpd doesn't "look" in the database.