Upgrade from 7.x-2.0-rc1 to 7.x-2.5 fails

Hi,

what I did in order to upgrade an existing dev site based on Drupal Commerce kickstart:

1. enable Commerce Kickstart Search and required modules (which I don´t need) because otherwise the upgrade when running update.php hangs
2. replace all the files in the docroot except the sites dir with the files in the 7.x-2.5 package
3. run update.php, no errors so far
4. flush all caches
5. run cron. The status page now says: "Database updates - out of date. Some modules have database schema updates to install. You should run the database update script immediately."
6. run update.php again with the following errors: "Warning: Invalid argument supplied for foreach() in field_extractor_settings() (line 298 of [...] /sites/all/modules/contrib/field_extractor/field_extractor.module)." and "Failed: DatabaseSchemaObjectExistsException: Table cache_entity_message_type_category already exists. in DatabaseSchema->createTable() (line 657 of [...] includes/database/schema.inc)."

As said, this is an existing, almost complete (dev) site ready to go into production soon.

The checkout process is working and tested. The checkout form worked until I did step 5.

However when I run update.php again (step 5), the checkout process does not work anymore: when I add a product to the shopping cart it says that the product has been successfully added but the shopping cart is empty and the product does not show up in admin/commerce/orders/carts.

Where does the error in 6 come from?
How could this be related to the problem with the empty shopping cart?

Thank you for your attention!