Using control-center-1.0.6 makes windowmaker-0.60 a "non-gnome compliant" wm -- root mouse clicks no longer work and gnome pager refuses to start. With c-c-1.0.5, there are no problems. gnome-libs-1.0.14 gnome-core-1.0.9 WindowMaker-0.60 compiled with "--enable-gnome" etc...
I just tried the GNOME in the Lorax beta and the WindowMaker in the Lorax beta together, and didn't experience any problems. control-center doesn't have anything to do with a gnome-compliant window manager's GNOME interactions, so I think it may be your local installation of WindowMaker.