start /D [dir base path - path to batch file] /B [batch file command]
That will tell Windows to launch the app in a background process. I don't know if it will help with what you are doing. Shutting down Apache means you're shutting down PHP as well which means PHP may stop any child processes it has started.
If need be, you may need to have your batch file issue the "AT" command to schedule a task to run almost immediately (say 30 seconds) which then runs your batch program to stop/start Apache.