I think Unity for Linux is too dull, such as above, when I switching another window and close it, then the MenuItem is active.But after a little, it inactive again. So I worry about whether there is such a situation, too horrible.
If you're talking about what I think you are it's a bug. However there is a fix, open the about menu where it shows you unity version etc. Close and now your menus should be working. If you run a game they will grey out again, open the about menu again.