The location of file being opened isn't same in .exe as in the IDE.
Try adding a file dialog message that displays the current working directory inside the executable to see where it's actually looking for the file or
d=dir('excelFile.xl*');
fn=fullfile(d.folder,d.name)
Or, of course, you could hardcode in a specific folder if it isn't needed to ever change or use the uigetfile control to pick a file.
The use of the base file name without an extension is also problematic; what if the user changes which file format to use and then there could be multiple files which match the name; which xlsread chooses in that case isn't documented; similarly, what xlswrite chooses on output wouldn't necessarily match. You need to be much more precise in handling the file names.
xlsread and xlswrite have been deprecated; it is recommended to use readmatrix for numeric data instead.
