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1. I manually upgraded, uploading only the changed files as listed at http://codex.wordpress.org/Version_3.1.3, but the dashboard still says "You are using WordPress 3.1.2." (I upgrade in this way because of several customized files over 5 blogs; it's worked fine for 5 years.)

Looking at the modification dates, I found a few other newer files:

wp-admin/network.php
wp-includes/class-wp-xmlrpc-server.php
wp-includes/ms-files.php
wp-includes/version.php

Updating those files (obviously, the last one most of all) now gets me "You are using WordPress 3.1.3.'

2. But now, there is an error with every admin page:

Warning: call_user_func_array() [function.call-user-func-array]: First argument is expected to be a valid callback, 'send_frame_options_header' was given in /home/xxxx/public_html/blog/wp-includes/plugin.php on line 395

That error only arose after updating the above extra pages, although that may have been due to caches expiring, since none of those pages contains call_user_func_array, although it may well be more complicated than that.

Although admin pages show up, it appears to prevent new posts.

Where is the problem?

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thanks for this thread its informative for me

Thanks to all for share useful information.

Thank you for posting this valuable info about WordPress. You such a explore the issues of theme.

May I ask you how you added so many words?

Just type "Wordpress 3.1.3 upgrade issues fix" on Google and you would see a page that suggests fix.