This corruption will also occur when changing the default media player
(from banshee to rhythmbox).

Hence I suspect it might be an issue with the "preferred applications"
tool.

P.s.
Just to be curious:
Is the "x-scheme-handler" supposed to be adjusted by adding/changing an 
appropriate line in ".local/share/applications/mimeapps.list" ? Or should I 
look somewhere else?

The setting in gconf "/desktop/gnome/applications/media/exec" does show
the correct change.

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https://bugs.launchpad.net/bugs/800927

Title:
  setting thunderbird as preferred email application corrupts "Launch
  Web Browser" shortcut

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