Experiencing the same behavior in Onereic x64 with Empathy 3.2.0.1.

I'm going to try @mightye's suggestion to see if new chat windows will open 
when receiving a message.
* Check "Open cats in separate windows"
* Uncheck Display incoming events in the notification area.

I'll post back once I see if this works with my setup.

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https://bugs.launchpad.net/bugs/206547

Title:
  Open (but do not raise) new conversation windows automatically

Status in Chat app, and Telepathy user interface:
  Fix Released
Status in GNOME Shell:
  New
Status in One Hundred Paper Cuts:
  Fix Released
Status in “empathy” package in Ubuntu:
  Fix Released

Bug description:
  Binary package hint: empathy

  On up-to-date hardy amd64, when I receive a message, the tray icon
  start blinking but the message is not shown. I have to click the tray
  icon to see it on a new window (or an open window, depending on my
  confs). This is very annoying, specially if my panel containing the
  tray is set to autohide. There should be an option to open messages
  automatically and/or a better visual message notification (like
  pidgin's guifications).

  Design "spec": https://wiki.ubuntu.com/OneHundredPaperCuts/Spec/206547

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