I had this issue myself on a custom theme I was building where the comments area would not display at all – even when all the comments code was properly set up like so:
if ( comments_open() || get_comments_number() ) :
comments_template();
else : echo 'Sorry, comments are not working right now.';
endif;
I was heavily using custom post types and custom fields in this theme, so the theme files included a lot of queries to pull in the custom content.
The issue for my theme was the fact that I was not always resetting WP_Query after each custom query.
wp_reset_query();
If you find that nothing else seems to work, just take a look through your theme files and make sure any custom query is always reset when you are done using it. That solved the issue for me and I hope this helps!
