There's no errors in the server log? Can you install a fresh intall of XenForo (not on your site, but in a development area obviously), and see if the xf_thread database scheme are all the same. Make sure your /library/XenForo/DataWriter/Discussion/Thread.php matches the fresh install.
@Mike found the answer and solved my issue. He says that when the uninstall failed, it did not remove or deactivate the template modifications that were still associated with @Daniel Hood MultiPrefix addon.