System map? No that shouldn't be happening, you should be able to select a planet/star/object inside the system then when you're done you should be able to resume your original flight plan by either the correct key-binding or by looking at the bottom of the left hand nav panel to find the route again to resume it. Has always worked like that for me in 1.2 and below anyway. Just wish we could do something similar with the actual galaxy map, especially considering how long it takes to plot a route nearer the core anyway.