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After upgrading to 3.5, I discovered that navigation has disappeared outside of the main index page. Theme is TwentyEleven and I've verified that this still occurs after disabling all plugins.

<?php if ( $wp_query->have_posts() ) : ?>

    <?php twentyeleven_content_nav( 'nav-above' ); ?>

    <?php /* Start the Loop */ ?>

            <?php while ( $wp_query->have_posts() ) : $wp_query->the_post(); ?>

            <?php get_template_part( 'content-beers', get_post_format() ); ?>

    <?php endwhile; ?>

    <?php wp_reset_query(); ?>

    <?php twentyeleven_content_nav( 'nav-below' ); ?>

Live site page

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This code didn't change since Twenty Eleven's initial release. Navigation is only printed if your query has more than one page. Could that be it?

Since you are calling $wp_query->have_posts() rather than have_posts(), this suggests you are modifying or overriding the query, which may be confusing WordPress (and it's not WP's fault). (See When should you use WP_Query vs query_posts() vs get_posts()?.)

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Thanks, I will take a look at that link. The way I was doing it was compatible with 3.4 but not with 3.5. I verified that the link disappeared immediately after upgrade (I didn't upgrade with other plugins that may have caused the change either). – Adam Dec 17 '12 at 21:37
I streamline & modified the code to fit that logic (I think?) but still no luck on getting navigation links to show up: pastebin.com/vMxRN4tx – Adam Dec 18 '12 at 0:46

Winning code (had someone help & it looks like they more or less copy-pasted from the front page. Not sure why I had arranged it differently on the beers page to begin with...

<?php query_posts('post_type=beer&paged='.get_query_var('paged') ); ?>

    <?php if ( have_posts() ) : ?>

        <?php /* Start the Loop */ ?>

            <?php while ( have_posts() ) : the_post(); ?>

            <?php if ( 'beer' == get_post_type() ) {

                get_template_part( 'content-beers', get_post_format() ); 

            } else;


        <?php endwhile; ?>

        <?php twentyeleven_content_nav( 'nav-below' ); ?>

    <?php else : ?>
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