Hi Mike,
It seems it cannot be done. When an application is using a bat file to run a set of DOS commands windows will use a named pipe for the CMD.exe window. Now even if you can get the handle of the window by ensuring that the PPID of the CMD.exe is the calling application's PID, you still cannot intrude in the pipe. This is the inherent characteristic of any OS. They would not allow you to hook to the handle one the process is created. So I think it is impossible to do what I was thinking of.
Correct me if I am wrong.