Found a Fix to my missing tables problem.. hope this will help others!
I just recalled a previous problem where my db (MySQL) would not take a date time value:’0000-00-00 00:00:00′ since it is in Strict mode. I found a fix from this forum about a year ago (http://wordpress.org/support/topic/mysql-5-stricttraditional-fix-requesting-feedback?replies=4) This fixed my problem ..again!
I have similar problem. Previously on 2.9.2 and upgraded to current version per instructions and without any problems. Created a new site and only 6 tables were created: wp_xx_terms, wp_xx_term_taxonomy, wp_xx_term_relationships, wp_xx_postmeta, wp_xx_options, and wp_xx_commentmeta. Tried everything that was posted here and had same results.
Using WP MU 2.9 and saw the same problem you are seeing. Thanks for posting a fix. We tested it out and did not see any problems.
Good Catch!!
