Jakob,
Sorry it took so long for someone to respond!
If you are using TTools version 1.3.3 or higher, it should include an application called "Airport Collector," which updates the Traffic.bgl file to include all airports that exist in fs2002, whether they are used in the AI flight plans or not. Running the Airport Collector once should solve your problem.
Based on your account, it sounds like you are using the "cut and paste" method of adding flight plans. Nothing wrong with that, as long you are using caution about what you are trying to add. I've seen examples of "bad" flight plans posted on various web sites. These will result in all kinds of error messages as you try to compile.
Good luck!