This is — in some sense — impossible. There is a window. (You can see it.) Either the debugger is lying to you, or the window is unrelated to the window controller. Whichever it is, it’s worth investigating further.

BTW, in your XIB file for the preferences window, did you leave “Visible at launch” checked? It shouldn’t be, if you’re using a window controller, but OTOH I can’t see it having this result if you did.