Mission Control is the culprit
Maverick now enables the Menu Bar and Docking bars on each dosplay. As well, you can now set that each display is a separate 'Space' accessable through Mission Control. This seems to have resulted in making each display a completely separate entity, so each display works independently. When you move a window from one display to another, it displays it as if you had moved it off the display in a one display settup.
The advantages the new functionality gives is that there is now a Menu and Docking Bar for each display. This means you do not need a 3rd party app to hava a menu bar on each display, but does mean that you cannot have the one window spread over 2 or 3 displays. You can also set up separate 'Spaces' for each display.
If you do not want this new functionality go to System Settings->Mission Control and uncheck the 'Display have separate Spaces' option. You will need to re-login to have the setting applied.
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