What exactly mean "don't close properly"?
After clicking OK or Cancel the window goes blank but it remains open and doesn't react on clicking on the close button. Only closing the app will also close the window (pretty annoying).
I am experiencing not exactly the same thing but also a problem with the prefs dialog. If I close preferences with OK or Cancel, things seem fine, but if I click on the Geany main window while the prefs dialog is open, then the dialog disappears and Geany becomes completely unresponsive. I have to kill it using Windows Task Manager.
This is occurring with Geany 0.13 on Windows XP Home. I am not sure which GTK version I'm using, but I installed from the geany-0.13_setup.exe program.
John