Public bug reported:

I use the open-source Java image analysis program ImageJ
http://rsb.info.nih.gov/ij/ in my work.  When I enable compiz, ImageJ
windows are sometimes empty.  Windows may contain data or plugins.  In
addition, windows are not listed in the taskbar.

I'm using Sun's JRE from the repositories and everything else is updated
(Ubuntu Hardy 64-bit).

My graphics card is an Intel 965, however other users of ImageJ have
reported this problem on nVidia cards.  One suspicion is that it may be
a problem with the gtk that the JRE uses, in which case we will redirect
this bug report to Sun.

The attached screenshot shows ImageJ and some of its windows open but
not listed in the taskbar.

** Affects: compiz (Ubuntu)
     Importance: Undecided
         Status: New

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ImageJ application windows empty when compiz enabled
https://bugs.launchpad.net/bugs/229824
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