Not sure if this may help I have been playing around for the last few hours with no luck but below is the code for the three files that call <? the_content(); ?>
Single.php
<?php get_header(); ?>
<div id="telo_blogu">
<?php get_sidebar(); ?>
<div id="obsah">
<?php if(have_posts()) : ?>
<?php while(have_posts()) : the_post(); ?>
<div class="post" id="post-<?php the_ID();?>">
<div class="nadpis">
<div class="datum">
<div class="datum_mesic"><?php the_time('M') ?></div>
<div class="datum_den"><?php the_time('j') ?></div>
</div>
<div class="titulek">
<a href="<?php the_permalink(); ?>" title="<?php the_title(); ?>" class="h2"><?php the_title(); ?></a>
<div class="meta"><?php the_author() ?> <?php _e("in"); ?> <?php the_category(',') ?> <?php edit_post_link(__('Edit This')); ?></div>
</div>
</div>
<div class="text_clanku" align="justify">
<? the_content(); ?>
<?php link_pages('<div class="pages"><strong>Pages:</strong> ', '</div>', 'number'); ?>
</div>
</div>
<?php endwhile; ?>
<div class="comments-template">
<?php comments_template(); ?>
</div>
<div class="navigation">
<?php previous_post_link('<span class="tlacitka">« %link</span>') ?> <?php next_post_link('<span class="tlacitka">%link »</span>') ?>
</div>
<?php else : ?>
<div class="post">
<div class="nadpis">
<h2><?php _e('Sorry, no posts matched your criteria.'); ?></h2>
</div>
</div>
<div class="navigation">
<?php posts_nav_link('','<span class="tlacitka"><< Previous</span>','<span class="tlacitka">Next >></span>'); ?>
</div>
<?php endif; ?>
</div>
</div>
<?php get_footer(); ?>
<strong>Page.php</strong>
<?php get_header(); ?>
<div id="telo_blogu">
<?php get_sidebar(); ?>
<div id="obsah">
<?php if(have_posts()) : ?>
<?php while(have_posts()) : the_post(); ?>
<div class="post" id="post-<?php the_ID();?>">
<div class="nadpis">
<div class="datum">
<div class="datum_mesic"><?php the_time('M') ?></div>
<div class="datum_den"><?php the_time('j') ?></div>
</div>
<div class="titulek">
<a href="<?php the_permalink(); ?>" title="<?php the_title(); ?>" class="h2"><?php the_title(); ?></a>
<div class="meta"><?php the_author() ?> <?php edit_post_link(__('Edit This')); ?></div>
</div>
</div>
<div class="text_clanku" align="justify">
<? the_content(); ?>
<?php link_pages('<div class="pages"><strong>Pages:</strong> ', '</div>', 'number'); ?>
</div>
</div>
<?php endwhile; ?>
<div class="navigation">
<?php posts_nav_link('','<span class="tlacitka"><< Previous</span>','<span class="tlacitka">Next >></span>'); ?>
</div>
<?php else : ?>
<div class="post">
<div class="nadpis">
<h2><?php _e('Sorry, no posts matched your criteria.'); ?></h2>
</div>
</div>
<div class="navigation">
<?php posts_nav_link('','<span class="tlacitka"><< Previous</span>','<span class="tlacitka">Next >></span>'); ?>
</div>
<?php endif; ?>
</div>
</div>
<?php get_footer(); ?>
Index.php
<?php get_header(); ?>
<div id="telo_blogu">
<?php get_sidebar(); ?>
<div id="obsah">
<?php if(have_posts()) : ?>
<?php while(have_posts()) : the_post(); ?>
<div class="post" id="post-<?php the_ID();?>">
<div class="nadpis">
<div class="datum">
<div class="datum_mesic"><?php the_time('M') ?></div>
<div class="datum_den"><?php the_time('j') ?></div>
</div>
<div class="titulek">
<a href="<?php the_permalink(); ?>" title="<?php the_title(); ?>" class="h2"><?php the_title(); ?></a>
<div class="meta"><?php the_author() ?> <?php _e("in"); ?> <?php the_category(',') ?> <?php edit_post_link(__('Edit This')); ?></div>
</div>
</div>
<div class="text_clanku" align="justify">
<? the_content(); ?>
</div>
<div class="komentar"><?php comments_popup_link('No Comments', '1 Comment', '% Comments'); ?></div>
</div>
<?php endwhile; ?>
<div class="navigation">
<?php posts_nav_link('','<span class="tlacitka"><< Previous</span>','<span class="tlacitka">Next >></span>'); ?>
</div>
<?php else : ?>
<div class="post">
<div class="nadpis">
<h2 ><?php _e('Sorry, no posts matched your criteria.'); ?></h2>
</div>
</div>
<div class="navigation">
<?php posts_nav_link('','<span class="tlacitka"><< Previous</span>','<span class="tlacitka">Next >></span>'); ?>
</div>
<?php endif; ?>
</div>
</div>
<?php get_footer(); ?>