Somehow my problem appears to be solved after applying Service Pack 2 for Inventor 2012. The new context menu layout seems to be working now. Previousy the new context menu freezed my whole design screen and I wasn't able to fill in fields of the active commands. Had to press escape to close the command, then I was able to view the model again. Had to close Inventor and restart it again, when that didn't help, I had to reboot the system.
I noticed the same issue, and I think I have a 'solution'. The context (Marking) menu seems to only go off the screen if you right-click near the middle (vertically) of the screen. There seems to be a band about an inch and a half wide (on my monitor) where this happens. If you click in the upper or lower half of the screen, the context menu opens fine.
I just have to get in the habit of moving my cursor before clicking . . . ;-)