Thanks to @Fraser I tracked this behaviour being present in CMake version 2.8.11.2 but not in 2.8.12.2. However AFAIK there is no changelog entry in http://www.cmake.org/files/v2.8/CMakeChangeLog-2.8.12.1 mentioning any fixes to IS_DIRECTORY
I recommend using the min version to ensure consistent behaviour then
CMAKE_MINIMUM_REQUIRED(VERSION 2.8.12.2)