In MakefileGenerator::writeSubTargets the code section:
//don't need the makefile arg if it isn't changed
QString makefilein;
if(subtarget->makefile != "$(MAKEFILE)")
makefilein = " f " + subtarget>makefile;

This would simply not work when $(MAKEFILE) is not "Makefile".
Therefore this should be:
if(subtarget->makefile != "Makefile")
makefilein = " f " + subtarget>makefile;