I confirm this happens under fedora 10 aswell, with KDE 4.2.1 systray,
its not a skype only issue.

** Changed in: compiz (Ubuntu)
       Status: Invalid => New

** Summary changed:

- skype icon in system tray has garbled background
+ skype (and QT icons) in system tray become garbled with compiz running

** Summary changed:

- skype (and QT icons) in system tray become garbled with compiz running
+ skype (and QT application icons) in system tray become garbled with compiz 
running

** Description changed:

  Binary package hint: compiz
  
- When compiz is running the icon of skype  has a garbled background where
- it should be transparent. this occurs with both the Nvidia 177 and 180
- drivers, aswell with the system tray in gnome-panel and AWN. This occurs
- randomly and the only way to have the icon show properly is by replacing
- compiz with metacity.
+ When compiz is running the icon of skype aswell as other KDE apps become
+ either completly garbled in the systray or their background becomes
+ garbled where it should be transparent. this occurs with both the Nvidia
+ 177 and 180 drivers, aswell with the system tray in gnome-panel, AWN and
+ KDE 4.2. This occurs randomly in gnome, but much more frequently in KDE.
+ the only way to have the icon show properly is by replacing compiz with
+ metacity or kwin.
  
  Providing a screenshot. Please keep in mind that its usually worse than
  what it looks like on the current screenshot (will upload one once it
  goes haywire).
  
  
  Compiz Version: 1:0.7.8-0ubuntu4.1 on Ubuntu 8.10
  
  ProblemType: Bug
  Architecture: i386
  DistroRelease: Ubuntu 8.10
  NonfreeKernelModules: ath_hal nvidia
  Package: compiz 1:0.7.8-0ubuntu4.1
  PackageArchitecture: all
  ProcEnviron:
   PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  SourcePackage: compiz
  Uname: Linux 2.6.27-11-generic i686

-- 
skype (and QT application icons) in system tray become garbled with compiz 
running
https://bugs.launchpad.net/bugs/327000
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