Oh yeah, I've been having that exact problem too, I was going to post a thread about it. It started happening around a week ago or something, and my error log is full of stuff like this:
WordPress database error Duplicate entry '2496' for key 1 for query UPDATE wp_2_terms
SET term_id
= 2496 WHERE term_id
= 4275595 made by wp_insert_category, wp_insert_term, apply_filters, call_user_func_array, global_terms
WordPress database error Lost connection to MySQL server during query for query SELECT t.*, tt.* FROM wp_2_terms AS t INNER JOIN wp_2_term_taxonomy AS tt ON tt.term_id = t.term_id INNER JOIN wp_2_term_relationships AS tr ON tr.term_taxonomy_id = tt.term_taxonomy_id WHERE tt.taxonomy IN ('post_tag') AND tr.object_id IN (12598) ORDER BY t.name ASC made by require, require_once, include, get_header, locate_template, load_template, require_once, get_sidebar, locate_template, load_template, require_once, dynamic_sidebar, call_user_func_array, rp_widget, rp_getstring_related_posts, rp_get_related_posts, wp_get_post_tags, wp_get_post_terms, wp_get_object_terms
And also plenty of query errors like this
WordPress database error MySQL server has gone away for query SELECT option_value FROM wp_2_options WHERE option_name (...)
Related to several plugins I have. I deactivated them all just to see if one of them was causing the problem, but I still had that issue with the categories. Something must've affected these tables in particular since it's affecting only one of the blogs, the rest seem to be fine.
I read in another thread that it might be related to Simple Tags, and I was indeed using it for a while (not sure when I stopped using it), but it was deactivated a few weeks ago (Still is), so I have no clue, really.