I posted this over at vbulletin.com and I've been told that this bug is caused by vBSEO.
I have a few smilies defined with relative links (i.e. forum/lol.gif instead of http://domain.com/forum/lol.gif). They show up perfectly in posts, but they just display as red X's whenever I edit a post. Smilies that are defined with absolute links, however, do show when editing. Weird...
I know that I could just change the relative links to absolute ones in the ACP, but there must be something wrong with the WYSIWYG editor here...