update.php doesn't run when migrating from 5.x to 6.x

After migrating a site from 5.16 to 6.10, I had to run update.php manually. The task log shows that some of the update code did run, but only some db schema changes.

Here is what was done:

ALTER TABLE {cache} ADD `serialized` SMALLINT NOT NULL DEFAULT 0
ALTER TABLE {cache_filter} ADD `serialized` SMALLINT NOT NULL DEFAULT 0
ALTER TABLE {cache_page} ADD `serialized` SMALLINT NOT NULL DEFAULT 0
ALTER TABLE {cache_menu} ADD `serialized` SMALLINT NOT NULL DEFAULT 0
ALTER TABLE {system} ADD `info` TEXT DEFAULT NULL
ALTER TABLE {system} ADD `owner` VARCHAR(255) NOT NULL DEFAULT ''
ALTER TABLE {locales_target} ADD `language` VARCHAR(12) NOT NULL DEFAULT ''
ALTER TABLE {locales_source} ADD `textgroup` VARCHAR(255) NOT NULL DEFAULT 'default'
ALTER TABLE {locales_source} ADD `version` VARCHAR(20) NOT NULL DEFAULT 'none'
CREATE TABLE {cache_block} ( `cid` VARCHAR(255) NOT NULL DEFAULT '&#03... (Expand)CREATE TABLE {cache_block} ( `cid` VARCHAR(255) NOT NULL DEFAULT '', `data` LONGBLOB DEFAULT NULL, `expire` INT NOT NULL DEFAULT 0, `created` INT NOT NULL DEFAULT 0, `headers` TEXT DEFAULT NULL, `serialized` SMALLINT NOT NULL DEFAULT 0, PRIMARY KEY (cid), INDEX expire (expire) ) /*!40100 DEFAULT CHARACTER SET UTF8 */
UPDATE {system} SET status = 0 WHERE name IN ('watchdog')