This usually affects Linux users with a tiling WindowManager.



Please try the following command before starting the game:

export _JAVA_AWT_WM_NONREPARENTING=1

 

If it works and fixes the game for you, 

you should add it to .xinitrc to load this permanently,



In case it does not help, you are required to use the tool 'wmname' to spoof your window-manager to something supported. like: LG3D

 

Get and install the tool 'wmname' and then run:
wmname LG3D

and use the

java -d64 -jar StarmadeStarter.jar

command again.

 

Both solutions should fix it, 

which one you choose is more a thing of your own system philosophy and comfort.