SOLVED. After an hour of creating a new template in ME last night I figured out what was happening. When placing a squadron of AI F/A-18c's at Paphos and having them take off from parking spots 45-48 and saving the map I entered the mission and the AI were present. I exited back to ME and continued placing objects etc. Saved and entered mission and the AI disappeared again. Went back to ME and clicked on the AI squad. The parking spaces for them were changed. So it is not Missing the AI, for some reason ME just decided that the other parking spots were better.