The error "Unrecognized function or variable 'ctfroot'. Error in => runtimeinitializationChecks.m at line 23" 
that could occur during the initialization of Matlab runtime can be fixed as follow:

1.	Go to the c:\Users\<username>\AppData\Local\Temp\<username> folder and 
2.	Delete the mcrCache<X> folder (<X> for the version of the runtime), and then
3.	Run Matlab runtime setup again to reinstall it.

Credits to Adrien Jeannerat for finding the workaround!