I’m currently using DreamTemplate’s Color Paper Theme, but I noticed that the code for the index.php file messes up the rendering of the index page. To fix, you need to change lines 7 and 31 from

 <?php the_content(''); ?>

to

<?php the_excerpt(); ?>

Now, the template will render an excerpt instead of the actual post on the main page. That will prevent the featured post from extending over the boundary as well as truncate the rest. If you just want to truncate the featured post, change only line 7.