Finally I found this threat because i'm having this issue too and it is driving me nuts.
I use the Notes app a lot since ML and there it happens all the time and lately I noticed it too with Mail. First of all, I can confirm that it is the "Hide Others" command and you can get the curser back in the application when you toggle between two windows in that app.
I experienced that issue only since ML, but here is another bug I try to solve where I don't know if it is related. It is very specific but I want to point it out. Maybe someone has an idea.
I'm using Logic Pro with an external controller Euphonix MC Control. I always have the issue that the touch display of the controller
looses its functionality during the day when I work in Logic and I have to restart the controller to get it back. I couldn't find the reason for it, all the trouble shooting didn't bring up anything and the now (Avid) customer support was of no help either. About two weeks ago, I finally stumbled over the needle in the hay stack. It was the "Hide Others" command which I use a lot. I can reproduce the bug 100% of the time. Using the "Hide Others" command will disable the controller's touch screen functionality.
Now you can imaging my surprise when I read about the "Hide Others" problem on this thread. I have to say that I had the problem with the controller and Hide Others already in Snow Leopard (maybe even Leopard), so this is not limited to ML like other people on this thread suggested.
Does anybody know if there is a Terminal command to disable the Key Command for Hide Others (opt+cmd+H). I use it all the time for years and it is almost a reflex that is hard to "untrain".