I don't think there is anything wrong with my default Paderborn. As I wrote Monday at 06:01 PM, I tried removing the Aerosoft Paderborn, and ran MkRwy (scanning only the default Paderborn). After this there were no issues with the file generated by MkRwy (no weird chars, and the xml loaded fine into the sim. I then reinstalled the Aerosoft Paderborn, and again I saw wierd chars. That why I said yesterday that I tough it was the "order" (default vs 3rd party Paderborn) ???
Anyway its working fine now, and I hope MkRwy can remain relevant for some time. Otherwise I hope Asobo/MS are planning to make APT-, RWY- and TWY-info available to 3rd party software some how. The Aerosoft CRJ 550/700 have just released for MSFS embedded with its own nav-data, but as far as I understand this is temporary and the plan is that in the future these 3rd party aircraft should have access to NavBlue data from within MSFS. But naturally that is only valid as long as the scenery is build according to these, and I doubt this will contain all info we have thanks to MkRwy ... time will tell.