RSS Feed Broken in 3.2.1

This logic is obviously messed up but there is no excerpt showing up anyway.

<?php if (get_option('rss_use_excerpt')) : ?>
		<description><![CDATA[<?php the_excerpt_rss() ?>]]></description>
<?php else : ?>
		<description><![CDATA[<?php the_excerpt_rss() ?>]]></description>

http://www.allnineyards.com/?feed=rss2

If I modify feed-rss2.php to use “<?php the_content_rss() ?>” then the field is populated with the post’s text; but all internal links and image URLs are put in to footnotes with a “[1]” left in their original position.
This is causing some rss readers and syndication systems to display those footnote indicators and ignore the images or URLs. GIGO I can’t change that behavior because the “make_url_footnote” function has been deprecated.

HELP!!!