Load .m file from a developed GUI (.exe)

I describe my issue more precisely: I developed a GUI that gets data from a binary file, does an FFT from data and plots magnitude and Angle when required by two callback buttons. The data is loaded from a Matlab script (.m) that loads the name of the binary file, using "run". This, as expected works when it is run into Matlab. However, I wanted to make an app (.exe) with this GUI, I'm able to build and package the app, but when I try to use it, I thing my data is not loaded and the plot function plots nothing. I'm using Matlab R2012a, does any one already have an issue like this?

Thank you beforehand for your help