WP 3.4 Breaks Captions

After upgrading to WP 3.4, all new captions do not render correctly.

seaslugteam.com

If you go there you will see the newest posts just have the caption right next to the image, whereas all older captions are properly styled underneath the image. I used the image uploader to add the images.

I am running Thesis theme, and if I switch to Twenty Eleven, the new captions display properly. The captions show correctly while within the visual editor as well. I suspect it is a theme issue with the new way WP handles captions, but how can I fix the theme to render captions correctly?

Things that I have tried that had no effect:
– deactivating all plugins
– resetting the plugins folder by FTP or PhpMyAdmin
– re-uploading the wp-admin and wp-includes folders from a fresh download

Looking through the HTML code, it appears that WP now strips some code out. There’s a missing class for alignment of the image, there’s no div around the image/caption, and there is no <p> (and thus no <p> with a unique class, either) or other HTML around the caption like there was prior to WP 3.4.

<dl id=”attachment_31587″ class=”wp-caption alignright” style=”width: 310px;”>
<dt class=”wp-caption-dt”>

Is stripped out according to another user, from this thread.