[rEd86]

The problem is the URL in the templates is relative, and since you've moved the articles.php to your root, the showthread.php file is not in the same folder. You need to add a fully qualified path to your forums folder, which will make all the links on the articles.php page fully qualified. The vBulletin variable that holds that path is $vbulletin->options['bburl'].

You need to replace all instances of:

<a href="showthread.php

with:

<a href="'.$vbulletin->options['bburl'].'/showthread.php

in the Article installation file and reinstall it. Or you can go in and manually update that text in all these templates:
af_articlebit
af_articlesmallbit
af_threadbit
postbit_display_complete

You need to update your branding as well to reflect the full path to your images. The same rules should apply to all instances of:

<img src="images

since that too is a relative path.

--Ed