I am running MATLAB with a command line string like this:
C:\\\\matlab.exe -nodisplay -nosplash -nodesktop -r \"run(\'C:\\
com.mathworks.mde.desk.MLDesktop.getInstance.closeCommandWindow
You can probably use it from the command-line as:
-r "com.mathworks.mde.desk.MLDesktop.getInstance.closeCommandWindow; run('C:\\mfile.m');"