I have two screens: 1440x900 on the left and 1920x1080 as my primary screen on 
the right. They are top aligned and the system tray appeared on top of the 
global menu on the panel and it was on the bigger screen only.
Replacing the GetGeometry() with GetAbsoluteGeometry() worked for me, see 
comment https://bugs.launchpad.net/ubuntu/+source/unity/+bug/778256/comments/12
This does not seem to be fixed in Oneiric (unity 4.14.2-0ubuntu1) and 
definitely not fixed in the latest Natty version 
(unity_3.8.16-0ubuntu1~natty2_i386)

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https://bugs.launchpad.net/bugs/778256

Title:
  Notification area ("system tray") missing when using dual monitors of
  different sizes, with their bottoms aligned

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