I had a similar problem recently with this 406 Not Acceptable error occurring when trying to update permalinks in WordPress. I also had the same problem when submitting any changes to the editor, etc. Google Webmaster tools would yield the same result.
The solution is to disable the mod_security firewall within your .htaccess
file.
My fix was to install a plugin called “WP Htaccess Editor” (free WP plugin), then update the .htaccess
file to the following, between the “Begin WordPress” and “End WordPress” tags:
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
Hope this helps.