OK I am having this same issue when sent to patrol and area.
Once I get a "Return to Base at your discresction" message, I need to stop sending messages and then return to base? I think I have done this and I get the message that my mission was incomplete????
What exactly does patrol an area mean? How big an area? Is there a specific pattern. I have yet to complete a mission that says patrol an area.
I've done the same thing the original poster said and it still says I did not complete the mission.
I even thought that saving the game might screw up my missions completion but that doesn't seem to be it either.
Give me the photo recon, deploy spies or saving downed pilots any day vs patrol an area.