The new Synergy project site has this bug here:
http://synergy-foss.org/pm/issues/27
And according to the site, it is fixed in 1.3.6. I have not yet
confirmed that the problem doesn't exist.
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Public bug reported:
Binary package hint: metacity
metacity 2.22.0 and others (package metacity 2.22.0-0ubuntu4)
Ubuntu 8.04 Hardy Heron and others
Gnome bug report: http://bugzilla.gnome.org/show_bug.cgi?id=567528
Java bug report: http://bugs.sun.com/view_bug.do?bug_id=6472274
Java windows
Patch from the Gnome bug adjusted for the 2.22 Metacity version.
** Attachment added: Patch adapted for 2.22
http://launchpadlibrarian.net/30513579/416058.patch
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Cannot raise windows from Java (toFront) - meta_window_same_application
improvement
https://bugs.launchpad.net/bugs/416058
You