Comment 3 for bug 591577

I *believe* that the reason is the following: seeing as applications running in the UNR environment are always maximized (by default) and that the Netbook launcher works on fullscreen, the only way the the system has to show (send to the top layer) the launcher when asked is by ignoring the 'always on top' flag of every other window.
The problem is that (A) it doesn't know that the other windows are in different displays and that they should not be touched OR (B) the launcher assumes that it is present in all of the displays, either way it doesn't work as one would expect.

@Jani Uusitalo If it helps, I work a lot with the netbook and a projector (second display) and the classic Ubuntu desktop did the trick for me. (That was the only workaround I found)