Upgrade to 2.6 – writing new tables instead of converting old

I’m upgrading to 2.6.1 from 2.3. When I run /wp-admin/upgrade.php I’m told that the database needs updating. During this process, the upgrade reports that certain tables are missing – ie, all the tables – and it creates them. Thing is, it creates them without the $table_prefix set in wp-config.php (which sets this to the default ‘wp_’. So it seems to ignore this setting (the wp-config.php script is the one from my previous 2.3 install). Yet it is obviously reading wp-config.php okay because it has access to the database. The result is a new, blank, blog with tables created without the prefix.