I had this problem too . It seemed to occur after an upgrade, I could add new accounts, and disable old ones, but unable to remove old accounts using the proper windows. I eventually found that account information appeared to be stored in the directory

/home/$USER/.config/libaccounts-glib/  (replace $USER with your username.) 

There where 3 files in there accounts.* ; I removed them all and rebooted the computer, and found all the online accounts where gone, I then re-created the new accounts manually as needed.

This is a bit of a heavy handed approach, so if you use it, I recommend you take a copy of the files before you remove them from that directory.

I had also this issue. It happend most if you start empathy on start-up with empathy -h.

I solved it to add killall empathy && empathy -h to startup. Sometimes even then it would not work. Then just open terminal and do killall empathy && empathy -h again.

Update1

I founded that program don't show up when you added empathy to the start up applications. You even not go online when added to boot. So remove it and start empathy manual after boot.