Redirection Issue

I just upgraded to 2.6 and now I am having issues accessing non-Wordpress directories. For example if I try to access the directory “twitter/api” on my server I am redirected to “2008/06/06/amazon-is-down/” or I receive a 404 error.

I am assuming this is a mod_rewrite issue but I am not sure. Is there a way to disable mod_rewrite for all non-Wordpress directories or any other fix?

This is a critical error because it breaks all my non-Wordpress applications hosted on my server.

Any input would be greatly appreciated. Thanks.