Some (all?) of the pop-up windows generated by this mod "click through" to underlying GUI elements.

Here's a reference to some ways to mitigate this issue:
http://forum.kerbalspaceprogram.com/index.php?/topic/144532-stop-click-through-in-ksp-11/

Also see: http://forum.kerbalspaceprogram.com/index.php?/topic/151354-unity-ui-creation-tutorial/

Should be fixed in release 0.7a0-mw9