Some installshiled installers with setup.exe have this problem, 7zip sfx do not work so well so I use WinRAR sfx instead, it does not have this problem One small note is that you should use two backslashes when in your config.txt to separate dirs ;!@Install@!UTF-8! GUIMode="2" RunProgram="MyApp\\setup.exe" ; Two backslashes \\ ;!@InstallEnd@! So yea switch to WinRAR sfx just for this or try start /wait, also try calling it via cmd file