SharePoint 2010 Notification Window Disappearing?
If you start heavily modifying the layout of your SharePoint masterpage, you might end up changing the z-index of different divs to achieve the design you are looking for. If you do this to the container div(s) that hold your ribbon, you might find that the notification window may start loading behind other divs. Luckily there is an easy fix.
All you should have to do is add the following CSS to your custom css stylesheet.
<span class="green">/*showing notification area / box flyout in case you are setting z-index elsewhere:*/</span>
Another tip, you might want to hide the notification window from anyone except with certain privileges. No problem, open your masterpage in SharePoint Designer and then use the
<<span class="purple">SharePoint:SPSecurityTrimmedControl</span> ID="SPSecurityTrimmedControl2" runat="server" PermissionsString="ManageSubwebs">