For anyone with a similar issue, I found a work around for now. Instead of sending inputs to the program via a textfile, I can enter them through keystrokes instead.
For my example, here is the code for my purpose:
h = actxserver('WScript.Shell');
h.Run('Program'); %Invokes Program.exe
pause(3); %Waits for Program to load.
h.AppActivate('Program'); %Brings Program to focus
h.SendKeys('~'); %Sends return
pause(5/100); %Waits briefly for program
h.SendKeys('A~'); %Sends A and return
pause(5/100); %Waits briefly for program
h.SendKeys('B~'); %Sends B and return
pause(5/100); %Waits briefly for program
h.SendKeys('C~'); %Sends C and return
pause(5/100); %Waits briefly for program
h.SendKeys('%{F4}'); % closes Program using Alt+F4
