As for the GUI problem; minimize the GUI once, it'll fix it .
As for recommended settings; I currently can't give you any to be frank. It's been a while since I've personally ran this.
Unfortunately, it's not something I can add in under 5 minutes, I have to overhaul quite some parts of the script which I'm currently not really planning on doing so. Sorry!
As @Chris stated, please consider learning the fundamentals of Java before proceeding with your scripting adventures. It'll most definitely be worth it to first master the required fundamentals.