It is not immediately obvious to me under which operating system you are running, but a word of caution seems in order. On Unix systems running Apache (for example), the userid under which CGI scripts run (often 'nobody' or 'webuser') is distinct from other more privileged userids and may not have the permissions to execute your batch scripts or open certain files. Also, the environment under which a webuser runs may be quite distinct (in terms of path and other variables) from a command-line user unless you explicitly set that environment. Whenever I hear someone say "It ran fine from the command line but not from the browser" I think of these two common problem areas.

The 'print header' and fatalsToBrowser answers you have received should help you identify any further problem that you may have.