Have you tried:
– deactivating all plugins to see if this resolves the problem. If this works, re-activate the plugins one by one until you find the problematic plugin(s).
– switching to the Twenty Eleven theme to rule out any theme-specific problems.
– resetting the plugins folder by FTP or PhpMyAdmin. Sometimes, an apparently inactive plugin can still cause problems.
– re-uploading the wp-admin and wp-includes folders from a fresh download of WordPress.
I did all of those besides re-installing the wp-admin and wp-includes folder. I did check to see if anything in that folder had changed, but nothing did. Here is the Error log…
[19-Jan-2012 13:52:23] WordPress database error Can’t create/write to file ‘/tmp/#sql_66a9_0.MYI’ (Errcode: 28) for query SELECT t.*, tt.* FROM wp_terms AS t INNER JOIN wp_term_taxonomy AS tt ON t.term_id = tt.term_id WHERE tt.taxonomy IN (‘link_category’) AND tt.count > 0 ORDER BY t.name ASC made by require, require_once, include, get_footer, locate_template, load_template, require_once, dynamic_sidebar, call_user_func_array, WP_Widget->display_callback, WP_Widget_Links->widget, wp_list_bookmarks, get_terms
[19-Jan-2012 16:00:11] WordPress database error Can’t create/write to file ‘/tmp/#sql_66a9_0.MYI’ (Errcode: 28) for query SELECT t.*, tt.*, tr.object_id FROM wp_terms AS t INNER JOIN wp_term_taxonomy AS tt ON tt.term_id = t.term_id INNER JOIN wp_term_relationships AS tr ON tr.term_taxonomy_id = tt.term_taxonomy_id WHERE tt.taxonomy IN (‘category’, ‘post_tag’) AND tr.object_id IN (2) ORDER BY t.name ASC made by require, wp, WP->main, WP->query_posts, WP_Query->query, WP_Query->get_posts, update_post_caches, update_object_term_cache, wp_get_object_terms
terms
I also cannot change categories and the site doesn’t show categories under the categories tab.
To upload the two folders from a fresh install, do I need to use the same version?
Yes – WordPress 3.0.1 in your case. You might also want to try repairing your database in case that’s where the problem is.