I am really no java guru but this seems code driven.
Now Dimlee, did you save/edit, save/edit/play, save/edit/play, save/edit a lot?
When I test airfields I do multiple edits of the one mission file which somehow, sometimes, after too many changes the becomes ... erratic. Typically you change the player aircraft to a different one and the game will just ignore it, even if it is correctly saved in the file.
It "feels" like problems you have with other software when you work for too long on the same file (MS Office 2003 or AutoCAD). This seems odd because we are only talking about a text file (not more complex file systems with internal, file specific database), but when I have this problem I just delete the mission and start from scratch.
On thing you could try is to create a new mission file, completely from scratch in a text editor, copy/paste the content of your original mission (the waypoints) and try it. This works for AutoCAD or Excel when files become uncontrollable.
Another thing you could do is save under different names as you do your changes, so that you can go back to the version before the problem appeared. There is no going back if you keep overwriting...