I had the strangest thing happen recently: when I fired up X11 in OS X (including wireshark, nomachine, etc.) and none of the modifier keys (control, and even shift!) would work. I poked around and found that System Preferences, Language & Text, Input Sources, had a direct effect. I had recently turned on Unicode Hex Input -- if one fires X11 up with this as the input source, the modifier keys won't work. Choosing "US" solved the problem... Hope this helps someone from beating their head against the monitor.