Exim by default will not trust any sending Users on your system (doesn't apply to mail sent via smtp). This means that any email sent as a User from a script will have the from address be set to user@server.hostname.com. If you wish to allow your Users to set the From address, and not have exim rewrite it, you can do so by setting this option:
untrusted_set_sender = *
in the top section of your exim.conf. This option is similar to the trusted_users option, except it doesn't give complete trust in the User.. it simply allows the User to set the sender as they desire.