If I do for instance: # USE="-X -opengl -gtk" emerge -p -e mplayer It correctly do not list Xfree86. When merging however, "/usr/lib/portage/bin/use" prints "X" and "gtk", etc, which means it thinks they are in USE even with the USE in: # USE="-X -opengl -gtk" emerge mplayer This is with portage-1.9.2 btw.
Fixed now, will appear in Portage 1.9.4.