When I go to "Staged Missions" | "Select Missions", the "Show Missions For All Terrains" should be UNCHECKED when I am in a Custom Arena or in the Offline Practice Arena.  95% of the time I am only going to want to see the missions for the terrain I already have loaded.  Make the default server the 95% case, not the fringe case.  That will probably lead to the least confusion.
$0.02.