I dont have a solution for the runway problem (except adding another runway on top of the one that causes problems) but I have an explanation.
NVA researched the nationality codes a few months ago and the result was that list with the number code for each nationality. Now you will probably remember that there are 2 numbers for each nation. the lower number means friendly, the higher one enemy.
This system has got advantages: e.g. you can have planes of the same nationality on the enemy and the friendly side at the same time, thats very useful for defector missions or any other mission in which u need planes from the same nationality to fire at each other.
On the other hand it causes some problems: In the MM file the airbases have a fixed nationality code. if the nation is by default enemy (in that map) the airbase has got the high (enemy) number code. Now if you change the side of the nation in question the airbase changes its colour in the map, but when the mission is loaded it will read the enemy code number from the MM file while the plane which is on the runway will have the friendly code number, even though airbase and plane are of the same nationality. Because of this the plane will not recognise the airbase as friendly and will not take off.
The same thing happens if its the other way round (a base which is by default friendly will not let enemy aircraft take off if the side of the nation has been changed to enemy)
adding a duplicate airbase over each of the bases works because the airbase will get its nationality code number in the mission file (i.e. not take it from the MM file) and this way the side of the airbase in the mission file will match the side of all objects from that nation in the mission.
About my Europe map: I haven't made any progress in the last month and Ill be busy for 1 more month. I will continue the project, but it'll take a lot of time