I have this bug as well, visible with some apt-get program, HandBake and
the Desura beta.

I know this patch is for a different bug, but the code looks like it might be 
able to help fix this:
https://code.launchpad.net/~njpatel/unity/fix-panel-tray

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https://bugs.launchpad.net/bugs/839354

Title:
  task tray icons are misaligned and badly sized

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