Steps to reproduce
===============
1. Add a resource -> link to a file or website

2. Insert whichever file you want
2.1 File link examples used (Doesn´t matter if they don´t existe):
        http://www.google.com/index.swf
        http://www.google.com/index.avi
        http://www.google.com/index.mp3
2.2 This doesn´t happen if you link to another HTML file.

3. Set the option Window: New Window

4. Save and return to course

5. Click on the newly created resource

6. Click on the popup link (the error is in the popup window)


Current output (with the extra </div>)
===============
<div id="page">
    <!-- END OF HEADER -->
    <div id="content" class=" clearfix"><div class="resourcecontent resourceswf"><object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"><param name="movie" value="http://127.0.0.1/moodle/file.php/3/Media_examples/muffins_from_space.swf" /><param name="autoplay" value="true" /><param name="loop" value="true" /><param name="controller" value="true" /><param name="scale" value="aspect" /><param name="base" value="." /><!--[if !IE]>--><object type="application/x-shockwave-flash" data="http://127.0.0.1/moodle/file.php/3/Media_examples/muffins_from_space.swf"><param name="controller" value="true" /><param name="autoplay" value="true" /><param name="loop" value="true" /><param name="scale" value="aspect" /><param name="base" value="." /><!--<![endif]--><a href="http://127.0.0.1/moodle/file.php/3/Media_examples/muffins_from_space.swf">http://127.0.0.1/moodle/file.php/3/Media_examples/muffins_from_space.swf&lt;/a&gt;&lt;!--[if !IE]>--></object><!--<![endif]--></object></div><div class="box generalbox generalboxcontent boxaligncenter"><p>Linking to a Flash file will see it displayed like this.</p></div><div class="popupnotice">(<a href="http://127.0.0.1/moodle/file.php/3/Media_examples/muffins_from_space.swf">Direct link to this file</a>)</div></div></div><div id="footer"><hr /><p class="helplink"><a href="http://docs.moodle.org/en/mod/resource/view"><img class="iconhelp" src="http://127.0.0.1/moodle/pix/docs.gif" alt="" />Moodle Docs for this page</a></p><div class="logininfo">You are logged in as <a href="http://127.0.0.1/moodle/user/view.php?id=2&amp;course=3">David Horat</a> (<a href="http://127.0.0.1/moodle/login/logout.php?sesskey=TYhwBRrrKK">Logout</a>)</div><div class="homelink"><a href="http://127.0.0.1/moodle/course/view.php?id=3">Features</a></div></div>
</div>

Other testing
===============
I have also tested this issue in http://demo.moodle.org/ and it happens there too.