I have encountered this once as well, and I somehow believe that it was because I loaded a savegame while there was a dialog window (alert, advisor, diplomacy, or something similar - I don't remember) open from the previous game.
Basically, I had just ended a turn, and at the beginning of a new turn there came some popup windows, but before they could appear, I pressed Ctrl-L to load a savegame, and while the Load Game dialog was active in the foreground, the end-of-turn popup appeared in the background (the game didn't freeze the end-of-turn processing in the background just because a Load Game dialog was activated in the foreground). I proceeded to load a savegame, but some part of the software seemed to become hung up with the end-of-turn popup that was never clicked away, so a "phantom modal window" was being carried on somehow indefinitely from a game which, from the software's point of view, was never properly ended.
And because the software kept thinking there was a popup that needed to be clicked away before other dialogs can proceed, it wouldn't allow me to do certain things any more.
I escaped the limbo state by exiting to Windows and restarting CivBE.
