Custom Permalink of Custom Post Type

If you are using Chrome to test this you will want to make sure your browser cache is emptied. Use the Chrome menu to empty the cache. This has bitten me more than once. I clear the cache, exit Chrome, re-access the site.

I've also had issues with Save Changes on permalinks not flushing the permalinks table. Change to the default post ID post type than back to your normal post type.

The other issue I've run into with my customer base is a WordPress theme that is augmenting the permalink rules. If not done correctly it can cause custom post types to malfunction. Try a default WordPress theme like Twenty Thirteen.

If all else fails start with a test site with a clean WordPress 3.6 install, add your custom post type and NOTHING else (no theme changes or extra plugins). That will eliminate all other variables and let you focus on server and system rules. Seems like you've already ruled that out, however.

Good luck & remember to share your answer if you find it on your own.

The issue is not due to WordPress configuration or PHP configuration. The reason of .htaccess not working is: In my Apache virtual host settings, it is configured to ignore .htaccess by:

AllowOverride None

To disable this lock, change the value in the virtual host file ( in sites-enabled folder ) to:

AllowOverride All

then restart Apache.