F5 and F9 key results difference

I was running a program1.m file

First I tried F9 and completed testing the code line by line and block by block (slect whatever line or block I needed then press F9)

After I found the entire code ready, I pressed F5. I have no idea, the result was not the same as it was with F9 execution

any thoughts

[Madhu Kodappully]

Here is the code: ctrlWindow is a Mex file. Window Name 1 is the result of program1.exe. Window Name 2 is the result of MATLAB GUI. When I click F9 after selecting the entire code, works great. Screens get switched. But when I do F5, there is window identification issue. MATLAB returns, unable to identify the window. Any thoughts?

% code begins

!program1.exe

ctrlWindow('Window Name 1',3);

pause(1)

ctrlWindow('Window Name 1',0)

pause(1)

ctrlWindow('Window Name 2',3);

pause(1)

ctrlWindow('Window Name 2',0)

pause(1)