Baffling phenomena with site-start.el

[Harry Putnam]

I've piddled around with this for a while today, just wondering why
this might happen.

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.

Too complicate things a
little.. /usr/local/share/emacs/site-lisp/site-start.el is a symlink
to a cvs protected file.

But, so is ~/.emacs

Further, by putting this: 
  (message "hello world -- from ~/.site-start.el") (sit-for 1)
At the bottom of both files (with aproppriate names to output)

I can see in *Messages* buffer that both are being loaded:
   (emacs /home/hgp/somefile)
  Loading disp-table...done
  Loading tool-bar...done
  Loading image...done
  Loading tooltip...done
  Loading ~/.emacs-custom...done
  Loading skeleton...done
  Loading advice...done
  hello world -- from ~/.site-start.el
  Loading help-fns...done
  Loading bbdb-gnus...
  Loading easymenu...done
  Loading bbdb-gnus...done
  Loading diary-lib...
  Loading regexp-opt...done
  Loading diary-lib...done
  Preparing diary...
  Loading holidays...done
  Loading cal-hebrew...done
  Loading cal-islam...done
  Loading cal-china...done
  No diary entries for Saturday, February 8, 2003 
  Loading ~/.abbrev_defs...done
  hello world -- from ~/.emacs
  (New file)

But still the line of code only works if I put it in ~/.emacs

Any one have and idea what I'm seeing here?