Although PHSETUP is executed from the command line, it is a Windows application. Consequently, it does not necessarily finish executing before the prompt returns unless you use the start/wait syntax: start/wait PHSETUP.EXE params
NOTE: If you call PHSETUP from a batch file or network login script and you want to have the entire script completed before returning the prompt, you must include the start/wait command in each line. If you use the @ control parameter so that PHSETUP executes the commands in a specified text file, each command in the file is executed in sequence. See “PHSETUP control parameters”.