I have the same problem and submitted the following feedback today.
How does one allow applications to be dragged "under" the menu bar to an external display arranged above the main display in Mountain Lion as works in Lion?
I have two laptops, each hooked to an external display arranged above the main display.
The menu bar is on the main display and I want it to stay there (because that makes it centrally located in the combined display area).
On my MacBook Pro Retina (mid 2012) using Mountain Lion (10.8.1), I CANNOT slide an application window from the lower (main) display under the menu bar and thus onto the upper (external) display.
On my MacBook (late 2006) upgraded to Lion (10.7.4), I CAN slide an application window from the lower (main) display under the menu bar and thus onto the upper (external) display.
Extensive web searches have turned up some complaints about the behavior I want to achieve, but no info on how to create it.
A thorough search did not turn up a "defaults" setting that appears applicable to changing this behavior. A search of my terminal history on the Lion machine reveals I did not issue any "defaults" commands to achieve its behavior; that seems to have always been its behavior. Ditto for the Mountain Lion machine.
This problem occurs irrespective of the application. It happens for Safari, Chrome, TextEdit, etc.
The older machine has had its OS upgraded twice. I suspect this (good) behavior may have been inherited from one of the older versions. The new machine came natively with Mountain Lion and has thus never experienced an upgrade. Or the problem is simply new to Mountain Lion.
I want to leave the menu bar on the lower display to reduce my "mouse miles"; it is more central there, appearing as it does in the middle of the combined display area. I know I could move the menu bar to the top of the upper display but that puts it too far from the dock and my primary, lower work area.
This works fine with the external display to the left or right or below the main display; the problem is clearly the menu bar itself. I bet the developers did most of their extended display testing with monitors to the left or right of the main display. For many years I myself was unaware the Arrangement with the external above or below the main display was possible.
By the way, the following works, up to a point. Start with a side-by-side monitor configuration and then move a window to the external display. Then re-Arrange, putting the external monitor above the main monitor. You can then slide the window up down and "behind" the menu bar as long as the title bar of that window does not go completely below the menu bar. The moment it goes fully below the menu bar, it is "trapped" and cannot go back up through the menu bar, which blocks it.