What happens if you double-click on the aircraft - does the map try to centre on the aircraft that's missing, or does an error message appear at the bottom of the screen?
I've tried to reproduce pjm's problem, but can't. Anyone else seen this problem? I find that if an aircraft has a distance shown in the aircraft list, it always appears on the map, immediately.
Here's an example, cycling through all aircraft displaying distance:
http://www.youtube.com/watch?v=uDHIYsFJ0P0I wonder if this is connected in some way to the alerts problem you're having.