1. make entries in four files according to the Administrator's Guide to create a
new mime type
2. try to start a file of this type from nautilus
3. see the mime type that is associated with this file in nautilus

4. to add is as a user via nautilus (right-click, associate with application)
doesn't solve this problem either, it is also reported in other bug reports on
this site.

Actual Results:
The mime type nautilus sees doesn't change

Expected Results:
The mime type should correspond with the entries/modifications I made

How often does this happen? 
always

Additional Information:
There seems to be a workaround and explanation to this. See also some bugs
concerning this in gnome-vfs etc.
There seem to be two places to store mime types, one comes from Gnome itself,
one from the integrated shared-mime-data from the freedesktop.org project. The
latter isn't mentioned at all in the Guide.
I can't tell if one of the modifications suggested in the Administrator's Guide
can be omitted (at least the /etc/gnome-mime-magic-data seems to do nothing),
but you need to also edit [on my system] the file in /usr/share/mime/packages/
and then update the freedesktop.org-shared-mime-database with
/usr/bin/update-mime-database.
With this modification nautilus sees the new mime type.