I haven't looked into why this only happens the second time I run the update, but right now I'm running into the following backtrace the second time I run update.php except that without my fix, the following line appears right after "...flow_revision table does not contain rev_user_text field."
The backtrace is
Adding index PRIMARY to table flow_wiki_ref ...A database query error has occurred. Query: ALTER TABLE `wiki1flow_wiki_ref` ADD PRIMARY KEY (ref_id) Function: DatabaseBase::sourceFile( /var/www/html/w/extensions/Flow/db_patches/patch-ref_id-phase2.sql ) Error: 1062 Duplicate entry '\x00' for key 'PRIMARY' (cihcisddb352v.corporate.ge.com:7780) Backtrace: #0 /var/www/html/w/includes/db/Database.php(901): DatabaseBase->reportQueryError('Duplicate entry...', 1062, 'ALTER TABLE `wi...', 'DatabaseBase::s...', false) #1 /var/www/html/w/includes/db/Database.php(3057): DatabaseBase->query('ALTER TABLE `wi...', 'DatabaseBase::s...') #2 /var/www/html/w/includes/db/Database.php(2978): DatabaseBase->sourceStream(Resource id #582, false, false, 'DatabaseBase::s...', false) #3 /var/www/html/w/includes/installer/DatabaseUpdater.php(669): DatabaseBase->sourceFile('/var/www/html/w...') #4 /var/www/html/w/includes/installer/DatabaseUpdater.php(742): DatabaseUpdater->applyPatch('/var/www/html/w...', true, 'Adding index PR...') #5 [internal function]: DatabaseUpdater->addIndex('flow_wiki_ref', 'PRIMARY', '/var/www/html/w...', true) #6 /var/www/html/w/includes/installer/DatabaseUpdater.php(455): call_user_func_array(Array, Array) #7 /var/www/html/w/includes/installer/DatabaseUpdater.php(420): DatabaseUpdater->runUpdates(Array, true) #8 /var/www/html/w/maintenance/update.php(179): DatabaseUpdater->doUpdates(Array) #9 /var/www/html/w/maintenance/doMaintenance.php(103): UpdateMediaWiki->execute() #10 /var/www/html/w/maintenance/update.php(224): require_once('/var/www/html/w...') #11 {main}
Patch incoming.