when you have eg a row of terminals in the upper half of your screen, mutter will place the control-center-shell window below them, causing the screen-height window to be halfway offscreen.

The problem is that we first map the window, and then resize it to the full height, so the mutter makes its placement decision based on the smaller initial height. 

One workaround might be to always map the window with the full screen height. (we can still do the size change we do now to tweak it, once the window is mapped).