I have a very similar problem to mikekmcguire's question about clamshell mode.
When connecting my MacBook Pro (Mid 2009 | 5,3) running Mountain Lion (10.8.2) to an external display in clamshell mode, the MacBook's display does not become inactive.
Thus, when moving my mouse to the edge of the screen (the right side in this case) it disappears onto the Macbook's display. This is a huge annoyance, especially when trying to use Hot Corners.
Going to System Prefs > Displays > Arrangement yields the following:
Here we can clearly see that despite the MacBook being in clamshell mode (external display is primary, lid closed, Apple logo LED off, external power/keyboard/mouse connected) – the MacBook's display is not being deactivated.
I know that I'm correctly in clamshell mode, and lifting the lid slightly reveals that the MacBook's display is indeed powered off.
My question is, is this a bug yet to be rectified in Mountain Lion?
Thanks in advance for any help/insight provided.