I noticed that display suite layouts outputted on the default front page or from views lose their contextual links ability. After some further research I discovered that this is due to the new $title_prefix and $title_suffix theme variables. These variables are usually wrapped around the node title in the node template and output the proper contextual links (among other things presumably). Since Display Suite overrides the normal node template these variables are no longer outputted.
I was able to restore functionality by simply printing out the two variables at the top of the display suite layout templates. I'm honestly not sure this is the correct way to go about it, but it seems to work.
At any rate:
// $Id: ds-1col.tpl.php,v 126.96.36.199 2011/01/13 20:14:50 swentel Exp $
* Display Suite 1 column template.
<div class="<?php print $classes;?> clearfix">
<?php print render($title_prefix); ?>
<?php print render($title_suffix); ?>
<?php print $ds_content; ?>