Steps :

1. Set up a Jabber account (let say adressname@blabla.net).
1bis. In the "personal information" window of the account, set a nickname
2. Join a Jabber chatroom
3. Make it a favorite
4. Activate auto-join for this chatroom

At this point, two possibilities :
a. If you join manually the chatroom using the menu, and you have the nickname set up at step (1) correctly. Everything is fine.
b. If you start Empathy (previously closed), the auto-join makes you join the channel. BUT the nickname you have is not the nickname set at step (1), but "adressname".

Note that it's not always the case, but almost all the time. And I had this problem as well on previous Fedora versions.

Thanks in advance =)