Comment 1 for bug 198528

Confirmed on Hardy, with Compiz enabled; there is still errant behavior as well when using Metacity, but Emacs is functional save for the fact that it refuses to minimize. This is also emacs-snapshot-gtk; I am not sure if regular emacs would experience the problem or not.

At first, it looks like when Emacs starts Alltray detects two windows, and the "real" Emacs window isn't the one being captured. If that's the case, then this isn't a bug in Alltray, per sé; it just means that to dock Emacs, one would have to always use Alltray in click mode, starting Emacs first, and Alltray second, and then grabbing the window. There are a few other applications that will do something like pop up a useless window first, and since Alltray latches onto the first window created by the application, that causes some side effects.

If this is correct (I or someone else will have to take a look at the Emacs sources to see if this is in fact the case), then this would be a bug only in that Alltray probably should have a different policy in the way that it attempts to intercept the events for applications.