I’ ve tried to repeat my own receipt Locate like command from the scratch and found no Qt/Root/QtRoot related issue.
However, there is a problem that is caused by some bug from cygiwn/make package. Sometimes the shell script to compile the long C++ package (like ROOT) can stop abruptly . In this case one just should restart the process. To do that do
source set_environment.sh
cd root
make
Normally one 
attempt suffices to complete 
the build.