Same problem over here, on Karmic with Matlab and with Weka (a Java data
mining tool). The windows are not listed in gnome-panel, until I click
the "click here to minimize all button" in the gnome-panel.
Linux desktop 2.6.31-17-generic #54-Ubuntu SMP Thu Dec 10 16:20:31 UTC
2009 i686 GNU/Linux
java version "1.6.0_16"
Java(TM) SE Runtime Environment (build 1.6.0_16-b01)
Java HotSpot(TM) Server VM (build 14.2-b01, mixed mode)
** Changed in: gnome-panel (Ubuntu)
Status: Incomplete => Confirmed
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java windows disappear from taskbar when filedialog is opened
https://bugs.launchpad.net/bugs/461822
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