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It began with version 3.7.1:

You are using WordPress 3.7.1. Update to 3.7.1

I've installed and usually update WP with git from https://github.com/wordpress/wordpress:

cd wordpress
git fetch --tags
git checkout 3.8

Then I usually download localized version (ru_RU) and copy over updated language files (wp-content/languages/).

Everything was smooth until 3.7.1 and it looks like I'm not the only one encountering this issue.

Does anybody have any idea how to fix that? Thanks!

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Have you tried just downloading the zip from wp.org? –  Andrew Bartel Dec 17 '13 at 21:07
    
Yep, tried simple update by hitting «Update Now» button @ /wp-admin/update-core.php. It updates and redirects me to awesome /wp-admin/about.php page but «Update Nag» still there. –  jibiel Dec 17 '13 at 21:41
    
What's the version number in wp-includes/version.php? –  Andrew Bartel Dec 17 '13 at 22:00
    
$wp_version = '3.8'; Checked that out too. Thanks for your time. –  jibiel Dec 17 '13 at 23:28
    
have you tried everything in the thread you linked? specifically, deleting everything in options table prefixed with _transient. –  Milo Dec 18 '13 at 0:34

2 Answers 2

Don't use the update now button, use a full on download of the core WP - http://wordpress.org/download/ - and then make sure you flush any cache you've got running. Do you have memcached or APC or xcache? Purge that. Plugins ditto.

I saw that on one of my sites where my server's object cache hung on to things. I went and checked the readme.html and verified I WAS on the right version, so I knew it had to be cached somewhere.

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I'd say flush server cache, browser cache then log out of WP. log back in after you flush everything. Should be fine. It's a cache issue most likely.

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