Just noticed that new mail notifications: 1. don't show new mail icon while mouse inside CM window -- it appears upon mouse leaving CM window. 2. don't clear when all new mail is read -- it only clears the new mail icon when the mouse leaves the CM window.
Are you sure it's not just trayicon implementation failing to redraw when necessary? It works just fine over here. (KDE 4.11)
May be related to this bug I filed against Mageia4beta(kde4.11.4): https://bugs.mageia.org/show_bug.cgi?id=12101