Tag/Category Pages Not Found

My friend is having trouble with the upgrade to 3.1. Once she upgraded, the tag pages and category pages do not show properly, as such here – https://animeyume.com/blog/tag/code-geass/.

When I took a backup of the database and restore it on my local test server on MAMP… same thing happens, which rules out a plugin error. In my php_error.log I found this:

[27-Feb-2011 18:47:09] WordPress database error Column 'taxonomy' in where clause is ambiguous for query
					SELECT wp_term_taxonomy.term_id
					FROM wp_term_taxonomy
					INNER JOIN wp_terms USING (term_id)
					WHERE taxonomy = 'category'
					AND wp_terms.slug IN ('my-favorites-lists')
				 made by require, wp, WP->main, WP->query_posts, WP_Query->query, WP_Query->get_posts, WP_Tax_Query->get_sql, WP_Tax_Query->_transform_terms
[27-Feb-2011 18:47:18] WordPress database error Column 'taxonomy' in where clause is ambiguous for query
					SELECT wp_term_taxonomy.term_taxonomy_id
					FROM wp_term_taxonomy
					INNER JOIN wp_terms USING (term_id)
					WHERE taxonomy = 'post_tag'
					AND wp_terms.slug IN ('events-2')
				 made by require, wp, WP->main, WP->query_posts, WP_Query->query, WP_Query->get_posts, WP_Tax_Query->get_sql, WP_Tax_Query->_transform_terms

I’m pretty sure something with the 3.1 upgrade has possibly mess up one of the entries in the taxonomy table… Any suggestions I should take to solve this problem?