On 02/14/2014 04:22 AM, Eli Zaretskii wrote:

Date: Fri, 14 Feb 2014 02:53:31 -0500
From: Michael Kifer <michael.kifer@stonybrook.edu>
CC: "16744@debbugs.gnu.org" <16744@debbugs.gnu.org>

Strange. When I run it with .emacs, then

M-x describe-variable ediff-highlight-all-diffs

returns

Documentation:
If nil, only the selected differences are highlighted.
Otherwise, all difference regions are highlighted, but the selected 
region is
shown in brighter colors.

But if it is started with emacs -q then the documentation string is not 
shown.

What is in your .emacs?

Lots of things. I need to see what is making the difference.

Anyway, can you explain why do we need _both_ defcustom and
ediff-defvar-local for the same variable?

ediff-defvar-local makes the var permanent local.