I am also using Ubuntu 10.04 with integrated Empathy (2.30.1) and I am having a 
similar problem. I have noticed that if I start my computer with a wired 
network connection at start-up then Empathy will connect to all my accounts 
automatically (without it being part of the start-up applications). I am 
guessing that the wired connection becomes established before Empathy has 
finished loading allowing it to connect. However if I start-up with a wireless 
connection (which I normally do) then the connection takes longer to establish 
and Empathy does not connect when the internet becomes available meaning that 
it does not to connect on start-up. For some reason, adding it to the start-up 
applications with the -h tag is an effective workaround for start-ups with 
wireless connections.
 
I hope this helps! It would be good in my opinion if Empathy was able to 
periodically check for an available internet connection and automatically 
connect. This way it would work as many people are expecting it to.

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empathy doesn't autoconnect at startup
https://bugs.launchpad.net/bugs/549723
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