I believe this is related to this bug.
I enabled empathy notifications by whitelisting the Empathy application. This is not exactly restoring 11.04 behavior but it is a workaround until the bug is fixed.
Here is how to accomplish this:
~ $ gsettings get com.canonical.Unity.Panel systray-whitelist
['JavaEmbeddedFrame', 'Mumble', 'Wine', 'hp-systray', 'Dropbox', 'scp-dbus-service', 'Skype']
~ $ gsettings set com.canonical.Unity.Panel systray-whitelist "['JavaEmbeddedFrame', 'Mumble', 'Wine', 'hp-systray', 'Dropbox', 'scp-dbus-service', 'Skype', 'empathy']"
Your initial list may look different than mine. Take note of the double quotes around the output list when passed as input as well as the new entry for empathy.
You will need to log out and login again for the changes to take effect.
Note: This is not ideal. On my box, when the old notification area blinks, it looks like it's missing the correct icon, but at least I know I have messages waiting. I am going to leave mine like this until they get Empathy working with the new notification area.