2.6.2 external integration

I’m running into an error when trying to integrate WordPress 2.6.2 with my external website and punBB forum. The exact error I get is:

Fatal error: Call to a member function set_prefix() on a non-object in /home/user/public_html/blog/wp-settings.php on line 216

It worked fine when working with 2.5. Is there something I’m missing? What was working was simply including wp-config.php from outside of the blog.

Thanks!
Ian

p.s. I saw this thread in the forums but it didn’t lead to an answer: http://wordpress.org/support/topic/174783?replies=11, so I’m opening a new topic.