I don't get automatically logged out (or at least none of the settings to do so), no file vault, etc, but I have just started to get this; from yesterday afternoon and over night this has started to happen.
I upgraded to Mountain Lion about 1 month ago (followed by Parallels Desktop and a couple of other things) and haven't (so far as I know) installed any new software since then. At least I have not had to enter my password to install anything.
Running an iMac with AMD Radeon HD 6970M.
I put it to sleep and turn off my magic mouse, as always.
Then after "some" time the system wakes, I am logged out, the system has no mouse connected so shows the message and I get a screen with my (logged in) desktop and the redraw behind the cursor (once my mouse it turned back on). I can then log in.
It has always turned itself on or made odd noises but only very occasionally and has never logged me out before.
I guess I need to find whatever it is that is logging me out whilst the system is asleep and sort that out! Oh the joy... just what I needed to do today.