I confirm that CTRL/ALT/SHIFT still do not work for me in WoW. I tried for example CTRL-TAB which is "Target Nearest Friend" and binding ALT+1 to an action bar button, neither work. However, it is also no longer passing the non-special key to the other WoW windows either - previously if you tried CTRL-TAB it would send TAB to the windows that do not have focus. It no longer does this.. so it seems its partially fixed at least.