I ran into a similar issue when creating Scottsdale Airport. I have Megascenery X Phoenix installed, and Megascenery likes to place unusual bgl files that can create chaos if you try to build scenery on top of it. I was eventually able to find the offending file and delete it (make sure you have a backup, just in case). It wasn't a big file, and as far as I could tell it just added an extra tower to Scottsdale even though it wasn't identified as belonging to that airport. Drove me nuts until I was able to figure it out.