I have got the same Problem :
Application I launch in second screen do not register in notification area(nto 
the first screen one or the second screen one).

If I launch the apps in the First screen it register to the 1st screen
notification area.

Ubuntu 7.04 beta Feisty Fawn 
DUAL DESKTOP mode
Linuk Kernel : 2.6.20-14-generic
2007 i686 GNU/Linux
Video Card : Ati X700
Gnome version 2.18.0

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Notification area does not work with dual head
https://bugs.launchpad.net/bugs/12696
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