1. Open Keyboard Preferences
2. Set modifier keys (I like to reverse option and command)
3. Log out
4. Log in
5. 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.