Ah, wow, I didn't notice the preferences dialog was part of the editor in your screenshot - I see nothing like that on my machine, all dialogs are separate windows. I have no idea how this could have happened - I'd suggest what Matthew says to e.g. rename the Geany configuration directory so Geany recreates it with a clean configuration (please keep the old configuration files and if the above helps, send us the geany.conf file so we can check what got wrong).
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