Random guess at what is going on. An app with an rgba colormap can't embed in an rgb app and vice versa. I'm guessing the panel starts with an rgb colormap because compiz hasn't started at that point and then the notification icons automatically get an rgba colormap through Qt (I doubt they'd set one manually). In this case XEmbed fails and you get applets popped out. Does this only happen with Qt apps or does something like pidgin have this problem too?
Random guess at what is going on. An app with an rgba colormap can't embed in an rgb app and vice versa. I'm guessing the panel starts with an rgb colormap because compiz hasn't started at that point and then the notification icons automatically get an rgba colormap through Qt (I doubt they'd set one manually). In this case XEmbed fails and you get applets popped out. Does this only happen with Qt apps or does something like pidgin have this problem too?