I have the same bug:
Natty 11.04 64bit with Classical gnome
I think I found a solution.
The problem is the area dedicated to app icons: it is not resized
automatically, when a new icon comes (for instance skype's icon).
on the top panel:
-> Unlock notification area applet
-> resize it manuall
There is already an open discussion here:
https://bugs.launchpad.net/gnome-panel/+bug/767095
Anyway I found a solution for the time being. (ubuntu natty 11.04/64
bit/gnome2)
The configuration of my top panel is [from left to right]:
[Main Menu] [ Notification Area] [Indicator Applet Complete]
T