I'm just copy&pasting the report by the original reporter from Launchpad (bug #1049210) since a lot of people are having this issue but no attention is being paid by Ubuntu devs.

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The problem occures with the combination of gnome-shell and empathy but I had to choose only one package...

When I receive a message from someone through empathy (connected to google talk) and the window for chatting with that person is not opened yet, the notification trai contains an icon for that person but the text content is missing and empathy's chat window doesn't open but if you open it manually the text is there.
After replying in gnome-shell notification window you get all the new messages that the person writes afterwards without any problems but you never get the old messages.

How to reproduce:
Open empathy chat window (google talk).
Say something to someone.
When that person replies write him something back in gnome-shell notification window and then close the empathy chat window on desktop (or if the window isn't opened yet just double click on gnome-shell notification window and close empathy window then after replying).
When that person replies back you will only get the notification icon without the text. Also the notification window won't pop up from notification tray and empathy chat window won't open.
If the person writes something else the notification window will pop up as normal containing the text that that person wrote next (without the text that was written first).

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This was reported for another version, but I'm having what seems to be the same bug (or at least a very similar one) on 3.6.1. There is no text shown on first notification, just an empty bubble. But once a person writes you another message, this second message (and the rest that follow) is shown in the chat notification bubble.