I can confirm that this bug affects Scilab 5.3 betas.  All but one
scilab application window disappear from the gnome panel window list
whenever a modal dialog box is invoked.  A bug was already posted on
scilab bugzilla:  http://bugzilla.scilab.org/show_bug.cgi?id=8308.

** Bug watch added: Scilab bugtracker #8308
   http://bugzilla.scilab.org/show_bug.cgi?id=8308

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some windows do not appear in the window list
https://bugs.launchpad.net/bugs/144406
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