Apple - Support - Discussions - Changing modifier keys in keyboard ...
http://discussions.apple.com/thread.jspa?messageID=10091638#10091638
"Unplugging the dongle to my Logitech MX 1100 and then swapping my modifier keys worked. Just be sure to open the modifier keys window first."
Snow Leopard broke Control and Caps Lock swapping
http://troyandgay.com/blog/2009/08/30/snow-leopard-broke-control-and-caps-lock-swapping
"The problem turned out to be related to the wireless USB hub for Logitech’s MX Revolution (and others?) mouse. If you unplug it before you change the Modifier Keys the changes do take effect. You can then plug the Logitech USB dongle back in and everything works fine. I tried every combination of plugging my keyboard into my computer but the Logitech dongle was plugged into the back of my display so I didn’t think to try it. Michael Richardson figured it out."