Custom Taxonomy Posts Missing

After updating to WordPress 3.1 I cannot see any posts in a custom taxonomy on my site. Whether on a taxonomy term page or on the edit posts screen, posts in this taxonomy don’t show up. On the edit terms screen if I follow the link to the right listing the number of posts assigned to each term it says “no posts found.” Even posts added to this taxonomy after updating to 3.1 are affected by this problem.