Попробуйте запустить экзешник из-под командного интерпретатора, так же, как нужно запускать BAT-файлы:

If the executable module is a 16-bit application, lpApplicationName should be NULL, and the string pointed to by lpCommandLine should specify the executable module as well as its arguments.

To run a batch file, you must start the command interpreter; set lpApplicationName to cmd.exe and set lpCommandLine to the following arguments: /c plus the name of the batch file.