Stop button doesn't stop minecraft server instance.

[NethercraftMC5608]

HELP NEEDED!
I tried everything, I can't get anything to work, I am starting to lose hope, I have been troubleshooting for 2 days now.

I press the stop button, and it says it has stopped, but when I htop, I can see that the java instance is still running.
as I didn't notice this issue, my server has been overloaded by old instances of servers still running.
if someone can please give me a code that can stop the 'screen' session and the java session.
It will be much appreciated.

Photo to the problematic code: (inside /data/config.php/)

My speculations are that the session dies but the java process still runs, or the session cannot die until the java process is been killed or stopped.
EDIT:
Never mind it works. I used geraskalnas fork and it works "ok". there is still a prominent issue, the java process has to finish generating the world until it could quit, which I guess is ok.