Yess, exactly endl3ss  :). I've explained in detail how to fix the problem with the corrupted files.

It is important to move the "</SimBase.Document>" entry AFTER EACH Save of the flight/exiting PD3, to the end of your *.fxml File.

So for example, if you have save your B-52 Flight under "B-52 USAF" two files will be generated:

B-52 USAF.fxml
B-52 USAF.wx

So you have to edit the "B-52 USAF.fxml" how stated above and all runs fine.