What I mean is, you said you were using an existing ping script. You should be able to call the c:\blah\blah\app.exe command instead of the ping.exe command. Running applications doesn't require that you "cd" to the containing directory. cd is mainly meant for human interaction.
For example, to test your app.exe, you could open a command prompt window, remain in whatever directory it happens to open in, and type c:\blah\blah\app.exe (use the correct path of course). It should run the app normally.