I have just upgraded from 5.22 to 6.16 (running under Mac OS X Snow Leopard) and got a lot of warnings on the semaphore and menu_router tables, like so:
user warning: Table 'bnupgrade.semaphore' doesn't exist query: SELECT expire, value FROM semaphore WHERE name = 'menu_rebuild' in /Users/me/Documents/WebSites/bn/includes/lock.inc on line 154.
and like so:
user warning: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near ') ORDER BY fit DESC LIMIT 0, 1' at line 1 query: SELECT path FROM menu_router WHERE path IN () ORDER BY fit DESC LIMIT 0, 1 in /Users/me/Documents/WebSites/bn/includes/menu.inc on line 2099.
This does not seem to be a critical problem, since further down in Update #6020 there is a "create table menu_router" which has run successfully, while #6054 has a "create table semaphore", also fine. So far the site looks ok so I am continuing with the upgrade, but it is disconcerting to get these errors just the same.
I have previously done an upgrade from 5.22 to 6.15 and don't remember getting these problems (though my memory may be playing tricks)