In auto-indentation mode, despite me having the indentation type set to spaces in the preferences window, Geany is adding tabs. In other words, it is ignoring the indentation type option. This problem was not present in version 0.14, only in the latest version 0.16. Some more info on my system follows:
Geany 0.16, GTK+ 2.16.0, GLib 2.20.0
Further information: On the other hand, if I try to change the indentation type option in the main menu of Geany then it works properly. So it appears that the Preferences window is neither getting nor setting the indentation properties at all. The main menu though is doing its job properly.