Actually, it's even weirder than that.
It seems like when I ctrl-tab the first time, I see document windows only. Then if I go to the document window (via ctrl-tab) it puts me in one of the tool windows and then if I do Ctrl-Tab it shows only tool windows (no document windows).
Perhaps the problem here is that the tool windows are within my document windows - not separate from them. I think this is probably different from what your navigation control expects. I guess I need to give up on tool window Ctrl-Tab in my application. Is there another keystroke just for tool window navigation within a document window? Also, is there a way to go to the 'non-tool window' part of the window via keyboard?