Thanks for playing! I am trying to work all the UI issues out.
Could you expand on why the mouse restriction is an issue in windowed mode? It should unlock your mouse when you are in a menu; but if it's not locked during gameplay, you would constantly be clicking outside your window as you drag the camera around to look.. at least that is the case on Windows.
As for the graphical issues, i can't really debug why they happen, linux builds are not that reliable.