Ok, I’m not a WP expert, but I have fiddled around with several templates and 2 blogs. I’ve taken a look at the code you posted above, and compared it with the classic and default templates that come with the WP download, as well as several free templates I’ve downloaded. The order of your PHP statements doesn’t match any of them.
Here’s a link to a theme I was considering: Elegance Remix. Nice, not too complicated. Here’s the code from the index.php:
<?php get_header(); ?>
<!-- Container -->
<div class="CON">
<!-- Start SC -->
<div class="SC">
<?php if (have_posts()) : ?>
<?php while (have_posts()) : the_post(); ?>
<div class="Post" id="post-<?php the_ID(); ?>" style="padding-bottom: 40px;">
<div class="PostHead">
<h1><a title="Permanent Link to <?php the_title(); ?>" href="<?php the_permalink() ?>" rel="bookmark"><?php the_title(); ?></a></h1>
<small class="PostAuthor">Author: <?php the_author() ?> <?php edit_post_link('Edit'); ?></small>
<p class="PostDate">
<small class="day"><?php the_time('j') ?></small>
<small class="month"><?php the_time('M') ?></small>
<small class="year"><? // php the_time('Y') ?></small>
</p>
</div>
<div class="PostContent">
<?php the_content('Read the rest of this entry »'); ?>
</div>
<div class="PostDet">
<ul>
<li class="PostCom"><?php comments_popup_link('0 Comments', '1 Comment', '% Comments'); ?></li>
<li class="PostCateg">Filed under: <?php the_category(', ') ?></li>
</ul>
</div>
</div>
<!--<?php trackback_rdf(); ?>-->
<div class="clearer"></div>
<?php endwhile; ?>
<div class="Nav"><?php if(function_exists('wp_pagenavi')) { wp_pagenavi(); } ?></div>
<?php else : ?>
<h2><?php _e('Not Found'); ?></h2>
<p><?php _e('Sorry, no posts matched your criteria.'); ?></p>
<?php endif; ?>
</div>
<!-- End SC -->
<div class="SR">
<?php get_sidebar(); ?>
</div>
<!-- Container -->
</div>
<?php get_footer(); ?>
You can see that the order of the PHP statements is different than what you have listed. I won’t guarantee this is the problem, but I think it’s a good starting point for you to consider.
If you are unable to solve this, have you thought of finding a good WP template, and then simply trying to change the images and color scheme? This is generally what I do (while giving credit to the developer who created the layout).
I hope this helps.