Follow-up Comment #5, bug #24785 (project gnustep):
This is an issue for me as well. SystemPreferences does not quit. I'm
currently using Slackware 12.1 and GNUstep SVN, but this has happened with
every release since the previous stable release and Slackware 12.0.
It's only SystemPreferences that has this problem on my machine, I don't have
a comprehensive install of GNUstep apps though.
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