Ok, got it figured out. Thanks to some help from over at the joomla forums.
It was the Search Engine Friendly Url's. I turned that off, and the site's links started working again.
Then I turned it back on, and had to rename the htaccess.txt to .htaccess, and got my SEF's back.
So incase anyone has this problem, there's the solution.
The site is
www.flatoutjoint.com