Rip, the reason that the mission planner worked in Africa Corps, was because we didn't lock down flight ops in advance of the "Roll" signal. So, we had to gamble that people wouldn't abuse the system and roll without permission(although they could've if they wanted to). If you disable an aircraft(or multiple aircraft) right now, the mission planner won't let you submit a mission if it contains any of the disabled aircraft.
The real problem is that an arena variable, "CountryCanFly", does not work right now. So basically, right now we can either lock down flight, or we can allow use of the mission planner, but not both. If we lockdown flight right now, then the mission editor won't let you submit a mission if it contains any disabled aircraft/vehicles.
We're working with Pyro to try to get this remedied before Hostile Shores. The goal is to allow use of the mission planner, while still being able to prevent flight prior to the start of the scenario.