When using QSettins directly:
QSettings::setPath(QSettings::NativeFormat, QSettings::UserScope, "$HOME/.config");
which is default value,
QSettings will write to folder $HOME/.config

-but when QFileDialog::getSaveFileName(NULL ,"Save","X") will be used
it will create directory $HOME in current directory and write some stuff there - instead to real home, or at least QSettings should write to $HOME in current directory too.

Example attached, use on linux.