That may very well be the problem, especially since on shutdown/logout Windows 7 always shows some items not closing, even if none are left. But emacs is about 50-50 on closing while other things always go away.
GNU Emacs 24.3.1 (i386-mingw-nt6.1.7601) of 2013-03-17 on MARVIN
GNU Emacs 24.3.1 (i386-mingw-nt6.1.7601) of 2013-03-17 on MARVIN