The "fullcreen minimap" works as intended as long as you aren't within a capture point. If you are standing on a capture point, it closes whenever the point's capture status gets updated (default every .3 seconds).
I think it's a bug. I do not believe it should be flashing like it does. Looks bad and doesn't allow you to do anything. Pretty sure you are suppose to be able to pull up the minimap and look at it while in a flag cap zone. I believe that is the intended feature.