Well I'm an idiot - the fulltext index on page_text was missing from a default installation. It didn't break searches but probably slowed them down tremendously. Also set engine to MyISAM on page_text to avoid cryptic error messages from MySQL.

<?php
class Text_Wiki_Render_Plain_Include extends Text_Wiki_Render {    
    function token()
    {
        return '';
    }
}
?>