It's not that difficult to reproduce, at least for me. The steps I take:
1.) Open Empathy (Applications > Internet > Empathy IM Client)
2.) Click Chat > Add Contact...
3.) For the Account drop-down list in the dialog box which appears, I have 
selected "New Yahoo! account". I move to the Identifier field and enter the 
identifier for a friend of mine ([[email protected]). Once I finish typing, 
this is automatically copied over to the Alias field and it allows me to select 
a group. I click on the Friends group I have previously set up, then go back to 
the Alias field and change it back to my friend's real full name. An icon now 
appears below the field marking her as "Offline".
4.) I click the Add button and the dialog closes. She now appears by her alias 
name in the Contact List window under my Friends group.
5.) Now I could just shut down, restart or log out of my computer, or even 
select Chat > Quit on Empathy's Contact List window. The results will be the 
same. The next time I restart Empathy and look in my list, all of my other 
contacts that I had previously entered into my groups are still there, but the 
new contact has mysteriously disappeared.

This behavior is exactly the same for me both on my laptop with Empathy
2.28 and on my desktop which is now running Empathy 2.30.

-- 
Empathy allows no more than 3 contacts per group upon restart
https://bugs.launchpad.net/bugs/561935
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