Joomla is very duplicate content challenged. I wrote a blog post about it a while ago, but I won't link to it so I don't look like a spammer. Here are the highlights:
1. The natural installation of Joomla comes with silly things like "print" and "pdf" icons. Both of these will lead to duplicate content issues.
2. Joomla's categories will lead to duplicate content
3. Different URL structures will lead to duplicate content issues
Still, not being indexed for the branded terms is a tough thing to be a part of. What is the niche you are in? Could you possibly be black listed? Is the domain new or did he buy it "used"?
