I recently upgraded from v3.2.1 to v3.3.1. I checked my Archives page today and found that <?php the_excerpt() ?> doesn't display excerpts from posts after I did the upgrade, but does show them for posts made before.
Here's my link:
If you view this, posts made between today (10th Jan 2012) and 30th December (around the time I upgraded) have no excerpt, but if you click "older entries" at the bottom, excerpts start appearing on December 29th and before. The format of the posts hasn't changed - I use a standard HTML template for all posts (and you can verify this by viewing a post that displays an excerpt vs one that doesn't) - and the only thing I can think has changed is doing the upgrade. For all the entries where an excerpt displays, it shows everything before the <!--more--> code as expected.
The code in archives.php is:
<div class="entry"><?php the_excerpt(); ?></div>
If you view the HTML of the generated page, you'll see this div has empty content for the posts where no excerpt shows.