The problem goes away if I remove the jakarta-cli.jar I have installed in /Library/Java/Extensions. There should be a way to configure Cyberduck to only use its own version. I need to have this installed for numerous java projects I use.
I'll try updating to a newer version to see if that fixes the problem, but if possible, Cyberduck should handle these errors instead of just logging an error to Console and showing no response to the New Browser menu item.
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All libraries installed into /Library/Java/Extensions take precedence in the classpath for any application using Java. You should install the dependency for the given application by putting it into the application bundle only as we do with all dependencies in Cyberduck.app/Contents/Resources/Java. Try to avoid a dependency hell.