What's the difference between deploytool and mbuild, mcc?

Hi, I'm not sure if this is the correct forum, but could anyone tell me the difference between Matlab's deploytool and the command line options mbuild, mcc? I'm trying to package a code using each of them, but the two options seem to act differently.

If I use deploytool, the exe only seems to run the first program, graph.m. That is, it plots the first function in a new window (but does not display the subtraction). Running mbuild and then mcc creates an executable that also opens a command line window, where the display('') and input commands take place. It also plots the second file. Any ideas why this happens?

I'm using Windows 7, Matlab R2013b, and my compiler is Microsoft Visual C++ 2010 in C:\Program Files (x86)\Microsoft Visual Studio 10.0.

----------

    function graph
    set(0,'DefaultFigureVisible','on'); %Ensure figures visible
    a=[12,54,33,80,26];
    b=[44,25,72,98,66];
    display(a-b)
    plot(a,b);
    plot([1,2,3,4,5],[1,2,3,4,5]);
    pause(2);
    graph1;
    end

----------

    function graph1
    name=input('name the graph:','s');
    plot([1,2,3,4,5,6,7],[1,2,3,4,5,6,7]);
    title(name);
    end