On resolution 1366x768 overview and codex window is too big: http://wstaw.org/m/2013/12/12/plasma-desktopVd3385.png
Your screen is stretched vertically for some reason... not sure what's going on, but you're not running with 768 pixels of real vertical resolution there.
The game resolution being slightly smaller than monitor resolution on Linux is a known and reported bug #58.
Could you give me link to this bug?
http://ludeon.com/mantis/view.php?id=58