We had a bug report on this in-house (for the Mac version only, I should note), and for a long time had trouble reproducing it. We finally were able to reproduce it in certain cases by opening Mathematica by double-clicking on certain notebooks, and we believe the problem has been completely fixed in v9. No new reports have come in against v9.
But, looking back in the history of the bug report, it looks like there were several cases where, for some users, the specific trigger for the behavior could never be properly ascertained, even though we were able to identify the bad state Mathematica ultimately entered that disabled the Quit item. So, I'd say that if you're launching Mathematica by double-clicking on a notebook, try not doing that. But possibly that's not what you're doing, in which case I'm not sure that I have much good advice to offer in the way of a workaround.
John Fultz email@example.com User Interface Group Wolfram Research, Inc.
On Mar 16, 2013, at 2:13 AM, Bob <firstname.lastname@example.org> wrote:
> I just installed Mathematica 8.0.4 on OS X Mountain Lion and noticed > that when I run it (without any apparent problems), now the "Quit > Mathematica" is greyed out and won't let me exit out of Mathematica. > Any ideas or suggestions? I can always force quit it, but really hate > to in case it causes problems. > > Thanks very much... > > -Bob >