Hey Capt Haplo
I got your email, sorry I had not replied by now, just been to damn busy to be on the PC.
The neutrality of the airbases is usually a product of the timeline. A base may be neutral, but once the nation enters the war, it is then allocated to a particualar side.
At the top of the editor is the date, if you move the date forward with those boxes, it will change the protagansts side to match the date. This is effectively so you can see how your .mis file is moving along without having to play the game.
Give that a try and post back here if there are any more issues. Don't feel you can't email me either, like I said earlier, just been busy. Not ignoring you