Hi Willie,
I just tested starting MATLAB R2016a with your command-line arguments on my Debian 7 machine with XFCE. On my machine, the plot windows were indeed disabled, so I was not able to reproduce the issue you are having.
One suggestion is to make sure that your Linux distribution is supported. You can find out the systems MathWorks supports MATLAB on here. If your system qualifies, I would suggest contacting MathWorks Technical Support to see whether or not the issue you're encountering is a bug. If it does not qualify, then my suggestion would be to look into obtaining a compatible version of Linux to run MATLAB on.
I noticed from the screenshots that it looks like you're using a tiled window manager. Off the top of my head, I wonder if that is causing an odd interaction with the -NoFigureWindows option. Could you try the startup command with a different desktop environment if you have access to one? I definitely advise you to contact Technical Support if your version of Linux is supported, as we will be able to help resolve your issue in a more systematic fashion. Hope this helps!
