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answers:

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I've updated my drupal installation and drupal modules, but admin/reports/updates says that Drupal version is still 6.12. To update drupal I ran - drush updatecode - drush updatedb (this updated only modules and said code still needs to be updated manually). Then I uploaded core, unzipped it, allowed to overwrite older versions and again ran - drush updatedb to enable changes. Still, admin/reports/status shows not 6.13 version as expected, but 6.12 and says core is not secure. I even ran update.php script in the end, but still core is displayed in red as well as modules located at admin/reports/updates.

Is using drupal shell (drush) a good practice for updates? Why is status still displayed as unupdated?

A: 

Did you check that drush actually changed the correct files on your system. You may find it is misconfigured.

Jeremy French
For instance, new Views version 2.6 is present in views.info, but report status screen still shows 2.3. Still researching..
PHP thinker
What level of caching do you have on? Admin should flush caches, but something could be preventing that, you can clear all caches on the admin/performance page
Jeremy French