Hi,
I just had the same problem when upgrading from 2.3.3 to 2.5.1. It was because of this bit of SQL:
SELECT SQL_CALC_FOUND_ROWS * FROM $wpdb->comments USE INDEX (comment_date_gmt)...
The comment_date_gmt index wasn’t present in my database(s) because the WordPress user didn’t have the ALTER privilege. Some other schema changes had also silently failed.
Cheers,
Ian