I have some trouble with .jar java file association. Dolphin keep seeing them as zip archive, even if in system setting they are already set to start with java -jar.

You may need to look at the mimetypes as well. KDE applications will obey the mimetype, then the file extension. I do not know what the Java mimetype is.

It's mime type should be application/x-jar, or at least thet is "xdg query filetype" answer.