Setting up a clear: both after x amount of posts

using a counter variable in the loop?

principle:

if (have_posts()) :
$counter = 0;
   while (have_posts()) :
      the_post();
      the_content();
$counter++; if($counter%4 == 0) {
echo '<div style="clear: both;"></div>';
}
   endwhile; endif;

you won’t need to add the endif; and endwhile; anywhere, as they should already be part of your loop.

the only new code is:
$counter = 0;
(which you could put anyhwere before the while( have_posts() ) of the loop;

and:

$counter++; if($counter%4 == 0) {
echo '<div style="clear: both;"></div>';
}

which you add directly after the closing div </div> of your post.

however, if this explanation does not help, can you repost the code of your loop.php using a http://wordpress.pastebin.com/ as i personally just don’t download code snippets to check them.