Hi,
I recently Installed Lion and found the same issue.
I then discovered that windows only overlap when one or more of the programmes are maximized to fill up the screen (in my case, which is maximized via the programme "Cinch"). When they all are restored by pressing the green button (the zoom button), they will be grouped back to their groups.
As I acknowlege it might be an issue due to Cinch, I uninstalled it and restarted the computer.
For the first time since the restart, overlapping still occurs, but soon after I press the zoom button, and resize them into the maximized window (without using Cinch, and apparently I've removed it), Wah-la, Mission Control is restored back to normal.
I wonder if any of you have installed Cinch. If yes, try to uninstall it. If not, see if you've got any incompatible software or Mods which have messed up the OS's ability in acknowledging the window size. I think it is a problem which the third party software has bypassed Mac's resizing function and therefore not being able to be recognized as maximized, thus overlapping others by their large thumbnail size.
Good luck!