I've been tripping along back to Texas from Georgia. After launching out of Columbus Metro the ATC sub-program? gave me the "no messages to transmit" screen. I flew through a controlled area and landed at an uncontrolled municipal and saved the flight. Now the ATC program is STUCK at "no messages"! What I had to do was load a different saved flight and move it to the muni to continue the trip with ATC functioning.
Try running the repair thing on disc one; always worth a shot!
Don't think I need to, the "glitch" was associated with only one of three saved free flights.