Hey Jules -
I just noticed that all the showMessageBox type methods (which add a modal dialog to the desktop, of course), don't ever bring that dialog to the front.
This can be potentially a problem, since if calling the function from a window which is set to be AlwaysOnTop, the AlertWindow then shows up behind the current window.
Haven't really dug into it, since I'm pulling all the Alertwindow stuff out of my code, but thought you might want to know. I think it would be a simple fix just by adding some bringToFront calls in there somewhere.