Logging out and in resets modifier keys to defaults Open Keyboard Preferences
Set modifier keys (I like to reverse option and command)
Log out
Log in
Modifier keys have been reset to defaults


I just upgraded from 10.7.5 to 10.8.2, might be related.

Every time I open Keyboard Preferences, I see the following in my console:


  System Preferences[570]: [BluetoothHIDDevice][initWithHIDDevice] Unable to get Object ID from IORegistry


.. so that might be related.
Uninstalled Intellitype
Restarted in safe mode (hold shift)
Use Disk Utility to Repair Permissions
Restart


Seems to have fixed the problem.  Perhaps some config file wasn't writable?  Who knows ..