I see the same problem. I'm running 3.8.16-0ubuntu1~natty1. If I adjust
my layout such that the smaller screen is at the top edge, rather than
the bottom, then I see the icons fine.

Annoyingly the system tray is also always on the left screen, even
though I set my centre monitor to be my primary (xrandr --output
DisplayPort-2 --primary). The unity launcher DTRT, but the system tray
does not.

** Changed in: unity (Ubuntu)
       Status: Fix Committed => Incomplete

** Changed in: unity (Ubuntu)
       Status: Incomplete => Confirmed

** Changed in: unity
       Status: Fix Committed => Confirmed

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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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