Permalink and Website Intergration – loop no longer working

If i set Permalink to anything other than default it stops my PHP website intergrations from working.

On the php pages on my site I ahve used the LOOP system to display content from a set catagory.

Is there away I can still use this and have Permalink to something more freindly than a number.Hi thanks for you advice esmi, mod_rewrite is working on the server as far as I can see the htaccess file is updating. Not sure if I explained the problem correctly.

Our main website is http://www.plymouthcathsoc.org.uk and our blog is located at http://www.plymouthcathsoc.org.uk/blog/

Our news and events pages pull articles directly from the blog. On the blog there a category for news and a category for events (plus others.
our news page can be found here http://www.plymouthcathsoc.org.uk/news.php

The news page incude any article that is found in the news category (category 3) if Permalink is running on the default settings the url for the category is as follows http://www.plymouthcathsoc.org.uk/blog/?cat=3 however if i set permalink to say http://www.plymouthcathsoc.org.uk/blog/news/ the pagesz then tell me there no posts matching my criteria

The code I am using on the php pages is as follows

<?php query_posts($query_string . '&cat=3'); ?>
<?php if ( have_posts() ) : while ( have_posts() ) : the_post(); ?>

 <div class="post">

 <!-- Display the Title as a link to the Post's permalink. -->
 <h4><a href="<?php the_permalink() ?>" rel="bookmark" title="Permanent Link to <?php the_title_attribute(); ?>"><?php the_title(); ?></a></h4>

 <!-- Display the date (November 16th, 2009 format) and a link to other posts by this posts author. -->
 <small>Posted <?php the_time('F jS, Y') ?> by <?php the_author_posts_link() ?></small>

  <div class="entry">
    <?php the_content(); ?>
  </div>
	 <hr></hr>
<p></p>
 </div> <!-- closes the first div box -->

 <?php endwhile; else: ?>
 <p>Sorry, no posts matched your criteria.</p>
 <?php endif; ?>

If I turn on permalinks and set it to use something other than default do I need to change this line of code
<?php query_posts($query_string . '&cat=3'); ?>
Thanks
Damien

http://wordpress.org/extend/plugins/wordpress-seo/