Hi mate,
Apologies, I completely lost track of this thread and rudely did not respond to you!
Unfortunately, it appears that there may be a bug with this particular City or Save. I do not even have the two small placement dots for the sign on the airport. I have saved the game and attempted to build the Airport on a few different road types and in a different area but except for the additional runways, the story is the same.
Strangely, I removed all of the runways to see if I had indeed done what you suggested and blocked the terminal spots. I am now unable to re-add the runways!
Have you any further suggestions?