All links and categories show my recent posts - wordpress

Question

When I click on any link on my blog the page and URL changes but still shows my recent posts, this is a custom theme I created from the 2010 theme earlier in the year and was working perfectly until recently.
The blog is here my blog
I'm sure it is a fundamental issue, has anyone had the same issue?
I originally thought it was a permalink issue but when I change theme the blog works properly.
Code from the loop.php template:
<?php /* Display navigation to next/previous pages when applicable */ ?>
<?php if ( $wp_query->max_num_pages > 1 ) : ?>
<div id="nav-above" class="navigation">
<div class="nav-previous"><?php next_posts_link( __( '<span class="meta-nav">←</span> Older posts', 'twentyten' ) ); ?></div>
<div class="nav-next"><?php previous_posts_link( __( 'Newer posts <span class="meta-nav">→</span>', 'twentyten' ) ); ?></div>
</div><!-- #nav-above -->
<?php endif; ?>
<?php /* If there are no posts to display, such as an empty archive page */ ?>
<?php if ( ! have_posts() ) : ?>
<div id="post-0" class="post error404 not-found">
<h1 class="entry-title"><?php _e( 'Not Found', 'twentyten' ); ?></h1>
<div class="entry-content">
<p><?php _e( 'Apologies, but no results were found for the requested archive. Perhaps searching will help find a related post.', 'twentyten' ); ?></p>
<?php get_search_form(); ?>
</div><!-- .entry-content -->
</div><!-- #post-0 -->
<?php endif; ?>
<?php
/* Start the Loop.
*
* In Twenty Ten we use the same loop in multiple contexts.
* It is broken into three main parts: when we're displaying
* posts that are in the gallery category, when we're displaying
* posts in the asides category, and finally all other posts.
*
* Additionally, we sometimes check for whether we are on an
* archive page, a search page, etc., allowing for small differences
* in the loop on each template without actually duplicating
* the rest of the loop that is shared.
*
* Without further ado, the loop:
*/ ?>
<?php while ( have_posts() ) : the_post(); ?>
<?php /* How to display posts in the Gallery category. */ ?>
<?php if ( in_category( _x('gallery', 'gallery category slug', 'twentyten') ) ) : ?>
<div id="post-<?php the_ID(); ?>" <?php post_class(); ?>>
<h2 <!--class="entry-title"-->><?php the_title(); ?></h2>
<div class="entry-meta">
<?php twentyten_posted_on(); ?>
</div><!-- .entry-meta -->
<div class="entry-content">
<?php if ( post_password_required() ) : ?>
<?php the_content(); ?>
<?php else : ?>
<?php
$images = get_children( array( 'post_parent' => $post->ID, 'post_type' => 'attachment', 'post_mime_type' => 'image', 'orderby' => 'menu_order', 'order' => 'ASC', 'numberposts' => 999 ) );
if ( $images ) :
$total_images = count( $images );
$image = array_shift( $images );
$image_img_tag = wp_get_attachment_image( $image->ID, 'thumbnail' );
?>
<div class="gallery-thumb">
<a class="size-thumbnail" href="<?php the_permalink(); ?>"><?php echo $image_img_tag; ?></a>
</div><!-- .gallery-thumb -->
<p><em><?php printf( __( 'This gallery contains <a %1$s>%2$s photos</a>.', 'twentyten' ),
'href="' . get_permalink() . '" title="' . sprintf( esc_attr__( 'Permalink to %s', 'twentyten' ), the_title_attribute( 'echo=0' ) ) . '" rel="bookmark"',
$total_images
); ?></em></p>
<?php endif; ?>
<?php the_excerpt(); ?>
<?php endif; ?>
</div><!-- .entry-content -->
<div class="entry-utility">
<?php _e( 'More Galleries', 'twentyten' ); ?>
<span class="meta-sep">|</span>
<?php edit_post_link( __( 'Edit', 'twentyten' ), '<span class="meta-sep">|</span> <span class="edit-link">', '</span>' ); ?>
</div><!-- .entry-utility -->
</div><!-- #post-## -->
<?php /* How to display posts in the asides category */ ?>
<?php elseif ( in_category( _x('asides', 'asides category slug', 'twentyten') ) ) : ?>
<div id="post-<?php the_ID(); ?>" <?php post_class(); ?>>
<?php if ( is_archive() || is_search() ) : // Display excerpts for archives and search. ?>
<div class="entry-summary">
<?php the_excerpt(); ?>
</div><!-- .entry-summary -->
<?php else : ?>
<div class="entry-content">
<?php the_content( __( 'Continue reading <span class="meta-nav">→</span>', 'twentyten' ) ); ?>
</div><!-- .entry-content -->
<?php endif; ?>
<div class="entry-utility">
<?php twentyten_posted_on(); ?>
<span class="meta-sep">|</span>
<?php edit_post_link( __( 'Edit', 'twentyten' ), '<span class="meta-sep">|</span> <span class="edit-link">', '</span>' ); ?>
</div><!-- .entry-utility -->
</div><!-- #post-## -->
<?php /* How to display all other posts. */ ?>
<?php else : ?>
<div id="post-<?php the_ID(); ?>" <?php post_class(); ?>>
<h2 class="entry-title"><?php the_title(); ?></h2>
<div class="entry-meta">
<?php twentyten_posted_on(); ?>
</div><!-- .entry-meta -->
<?php if ( is_archive() || is_search() ) : // Only display excerpts for archives and search. ?>
<div class="entry-summary">
<?php the_excerpt(); ?>
</div><!-- .entry-summary -->
<?php else : ?>
<div class="entry-content">
<?php the_content( __( 'Continue reading <span class="meta-nav">→</span>', 'twentyten' ) ); ?>
<?php wp_link_pages( array( 'before' => '<div class="page-link">' . __( 'Pages:', 'twentyten' ), 'after' => '</div>' ) ); ?>
</div><!-- .entry-content -->
<?php endif; ?>
<div class="entry-utility">
<?php if ( count( get_the_category() ) ) : ?>
<span class="cat-links">
<?php printf( __( '<span class="%1$s">Posted in</span> %2$s', 'twentyten' ), 'entry-utility-prep entry-utility-prep-cat-links', get_the_category_list( ', ' ) ); ?>
</span>
<span class="meta-sep">|</span>
<?php endif; ?>
<?php
$tags_list = get_the_tag_list( '', ', ' );
if ( $tags_list ):
?>
<span class="tag-links">
<?php printf( __( '<span class="%1$s">Tagged</span> %2$s', 'twentyten' ), 'entry-utility-prep entry-utility-prep-tag-links', $tags_list ); ?>
</span>
<span class="meta-sep">|</span>
<?php endif; ?>
<?php edit_post_link( __( 'Edit', 'twentyten' ), '<span class="meta-sep">|</span> <span class="edit-link">', '</span>' ); ?>
</div><!-- .entry-utility -->
</div><!-- #post-## -->
<?php comments_template( '', true ); ?>
<?php endif; // This was the if statement that broke the loop into three parts based on categories. ?>
<?php endwhile; // End the loop. Whew. ?>
<?php /* Display navigation to next/previous pages when applicable */ ?>
<?php if ( $wp_query->max_num_pages > 1 ) : ?>
<div id="nav-below" class="navigation">
<div class="nav-previous"><?php next_posts_link( __( '<span class="meta-nav">←</span> Older posts', 'twentyten' ) ); ?></div>
<div class="nav-next"><?php previous_posts_link( __( 'Newer posts <span class="meta-nav">→</span>', 'twentyten' ) ); ?></div>
</div><!-- #nav-below -->
<?php endif; ?>

Answer 1

When you create a wordpress theme you must understand the Template Hierarchy or you'll have trouble setting page content. As you can see in the page I've linked wordpress has some basic rules that it fallows to display content from different template files. If one file is missing from the hierarchy, wordpress will fallback to the next one in hierarchy.In your case if you don't have category-{slug}.php the content displayed for a specific category will be the one generated by the category.php code.If you don't have category.php then wordpress will read archive.php and so on till index.php.If you want to display a specific loop make sure you have the code in the correct file and the file named with respect of the template hierarchy rules so it's code will run when you want it to run.

Answer 2

The reason my blog was showing the top 5 posts on every page was because I has the following line in the header file:
query_posts('showposts=5');
I used this in my main static part of the site so I could show the most recent 5 posts in my footer.
I have moved this code to my blog footer and all is working again.
Thanks for all your relpies.