Hi ! Excuse my bad english...
I have the same problem on two computers : I am on Ubuntu 12.04 32 bits, kernel 
3.2.0-32-generic-pae, package mail-notification 5.4.dfsg.1-5ubuntu1. 
Ubuntu 12.04 installed from nothing on the first computer and was upgraded from 
11.04, then 11.10 on the second computer. I use Unity on the two computers.. 
The popup window appears on different places. More I have messages, more the 
places are near the bottom of the screen. Less I have message, more the places 
are near the top of screen.

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https://bugs.launchpad.net/bugs/971909

Title:
  Popup window on mouse hover wrongly rendered and misplaced

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