your "Hack to fix a problem with Twenty Eleven custom excerpts" in file excerpts-highlights.php fails under several conditions.
First, if filter 'twentyeleven_custom_excerpt_more' has been removed previously (e.g. in functions.php) it will be always activated by your code after the first post found. You may use function
has_filter( 'get_the_excerpt', 'twentyeleven_custom_excerpt_more') to remove and reinstall that filter.
Second, if someone like me has removed filter 'twentyeleven_custom_excerpt_more' in functions.php and set an alternative 'more' filter this hack fails completely. For custom excerpts I get currently up to three more links.
Also the call to apply_filters('get_the_excerpt', $excerpt) should positioned after appending the closing ellipsis. Otherwise the ellipsis is appended after the more link.
The problem only occurs with custom excerpts and not with auto created excerpts. But any filter which adds a more link to a custom excerpt has to check for existence of that custom excerpt with function has_excerpt().
A solution may be to temporarily delete the value of $post->post_excerpt. Thus the call to
apply_filters('get_the_excerpt', $excerpt) in your plugin will not create an additional more link.
I've just testet this and it seems to work properly. Modify in function relevanssi_do_excerpt():
$excerpt_save = $post->post_excerpt;
$post->post_excerpt = '';
$excerpt = apply_filters('get_the_excerpt', $excerpt);
$post->post_excerpt = $excerpt_save;
(Delete all the code which adds and removes filters 'twentyten_custom_excerpt_more' and 'twentyeleven_custom_excerpt_more'.)
I hope this helps a bit and thank you for that phantastic plugin.