I've noticed that the problem occurs when mousing over a frame in a web page which was not the last frame the mouse was over. So, for example, opening up the addons window. I open it from the menu, and it opens up just fine on top of everything else. But when I move my cursor from the menu bar to the current web page (Thus moving across the current web page which is no longer in focus), the main window usually jumps on top of the addon window (Without stealing focus), which I have to bring back up from the task bar by minimizing and restoring it :/