Lyde: BesuGo has the correct file I think but jGoBoard is missing a stone
posetcay: I have no idea what is causing the problem with jGoBoard, but BesoGo will probably become the default option in the future and jGoBoard version will no longer be a problem.
The file had some weird tags etc. and it couldn't be even opened by on-site editor so I cleaned up the file and it works fine now.