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From: Eli Zaretskii <eliz@is.elta.co.il>
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Subject: Re: Baffling phenomena with site-start.el
Date: Sun, 9 Feb 2003 08:17:38 +0200 (IST)
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On Sun, 9 Feb 2003, Harry Putnam wrote:

> Briefly, the phenomena is that this line of code:
> (setq inhibit-startup-message t)
> Is ignored when inserted in site-start.el, but works (prevents splash
> screen) when inserted in ~.emacs.

This is by design.  The following fragment from startup.el should explain 
why:

    ;; Run the site-start library if it exists.  The point of this file is
    ;; that it is run before .emacs.  There is no point in doing this after
    ;; .emacs; that is useless.
    (if site-run-file
        (load site-run-file t t))

    ;; Sites should not disable this.  Only individuals should disable
    ;; the startup message.
    (setq inhibit-startup-message nil)

    ;; Load that user's init file, or the default one, or none.

As you see, the startup code forcefully resets inhibit-startup-message 
after it loads site-start.el, to prevent site administrators from doing 
exactly what you wanted to do.