slideshow markup no longer works after upgrade to 3.5

I updated to 3.5 recently and since that time, markup codes for a slideshow and audio player no longer work, and instead the codes are emitted to the browser verbatim and appear in the browser (see here).

The code from header.php in our default theme folder is:

<div id="mainimage">
    <?php echo do_shortcode('[slideshow id=1]');?>
</div>