After some experimentation I found that adding ‘FORCE’ to the ‘set’ commands fixed the problem. The text Professional CMake does not have this directive in the calls though.
Looking at the documentation for the set command shows that if the cache variable is already defined then a ‘set’ command will not over write it without FORCE. I rm -rf'd my build directory and re-ran the steps. All I did was declare my build type to be ‘Profile’, I did not define any variables.
So the remaining question is, does CMake auto generate and define these variables before my 'set’s get called?