Problem compiling my standalone application, which is connected with another program .exe

I use XFOIL (aerodynamics software for airfoils analysis) in my matlab standalone applications, so, my code "calls" xfoil depending on the input parameters (as angle of attack, type of airfoil, etc), when I try to compile the programm on the applications compiler, first on the section "files requiered for your applications to run" and "files installed for your end user", I add all my .m files, the .fig files (for the guide interface) and the xfoil.exe software file. When is already compiled and I run the programm and input the require parameters, the program always run incorrectly , the programm always appers to analyzed the same airfoil and angles of attack even if I change it , because always trow the same results, it looks like if the program always run with the last airfoil analyzed before compile the program or the first analyzed on the already compile program, like if the xfoil.exe software inside on already the compile program, save a input data and always run with the same, ignoring a new input data. On my personal Matlab the programm runs very good and does not have any error, I have tried to compile the programm with out the xfoil.exe application and them I add it to the folder of the compile app that creates matlab, but it does not work, any advice?