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.

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.