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a60fb26
(Get the code!)
I can confirm this behaviour, to aid in the troubleshooting, here are my notes on the subject.
had Jaunty 9.04 w/ compiz and ATI driver (FGRLX) and used Eclipse no prob.
upgraded to Karmic 9.1 and experienced Eclipse issue noted by Andrew Scherpbier above, GDK_NATIVE_WINDOWS does work around that issue.
turned off compiz to allow VNC connection, noticed this Window List panel behaviour.
re-enabled compiz, problem persists
I am up-to-date aside from the samba updates available past few days.
poopy to say the least.