*Any* plugin? Just adding a plugin to your forum makes threads disappear? Do you have plugins enabled currently on your site?
So, if you add the following plugin, the thread just disappears?
hook_location - process_templates_complete
PHP Code:
$template_hook['navbar_end'] .= '<li><a href="test.php">Test</a></li>';
And when you upgraded to vB4, did you delete all the old vB3 plugins/products first? Or did you upgrade them all after you upgraded the forum?