404 permalink errors on Pages only

Question

I am having a strange issue with permalinks while using the /%postname%/ structure.

I can access my custom post types using the pretty permalink localhost/cpu/<post-type>/<post-title>/ but I am getting a 404 error on Pages. The url of a page is localhost/cpu/<page-title>/

My .htaccess file (generated automatically when saving permalinks):

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /cpu/
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /cpu/index.php [L]
</IfModule>

# END WordPress

My WordPress(version 3.4.2) installation is in a folder called cpu. I don't have any issues with the default permalink structure url/?p=123. The problem does not go away when I disable all plugins.

Any possible solution?

Is there a way to debug what's happening?

UPDATE:

Following Code Monkey's answer, I added the following to functions.php I changed the filter from rewrite_rules_array to page_rewrite_rules - the WP_Rewrite Class reference suggests:

To filter the rewrite rules generated for your Pages, use page_rewrite_rules.

So, here's the code I added:

add_filter('page_rewrite_rules', 'rewrite_rules_array_filter_debug', 10000);

function rewrite_rules_array_filter_debug($rules){
  echo '<pre>';  
  var_dump($rules);
  echo '</pre>';
  return $rules;
}

And the output from saving the post permalinks on wp-admin/options-permalink.php:

array(11) {
  [".?.+?/attachment/([^/]+)/?$"]=>
  string(32) "index.php?attachment=$matches[1]"
  [".?.+?/attachment/([^/]+)/trackback/?$"]=>
  string(37) "index.php?attachment=$matches[1]&tb=1"
  [".?.+?/attachment/([^/]+)/feed/(feed|rdf|rss|rss2|atom)/?$"]=>
  string(49) "index.php?attachment=$matches[1]&feed=$matches[2]"
  [".?.+?/attachment/([^/]+)/(feed|rdf|rss|rss2|atom)/?$"]=>
  string(49) "index.php?attachment=$matches[1]&feed=$matches[2]"
  [".?.+?/attachment/([^/]+)/comment-page-([0-9]{1,})/?$"]=>
  string(50) "index.php?attachment=$matches[1]&cpage=$matches[2]"
  ["(.?.+?)/trackback/?$"]=>
  string(35) "index.php?pagename=$matches[1]&tb=1"
  ["(.?.+?)/feed/(feed|rdf|rss|rss2|atom)/?$"]=>
  string(47) "index.php?pagename=$matches[1]&feed=$matches[2]"
  ["(.?.+?)/(feed|rdf|rss|rss2|atom)/?$"]=>
  string(47) "index.php?pagename=$matches[1]&feed=$matches[2]"
  ["(.?.+?)/page/?([0-9]{1,})/?$"]=>
  string(48) "index.php?pagename=$matches[1]&paged=$matches[2]"
  ["(.?.+?)/comment-page-([0-9]{1,})/?$"]=>
  string(48) "index.php?pagename=$matches[1]&cpage=$matches[2]"
  ["(.?.+?)(/[0-9]+)?/?$"]=>
  string(47) "index.php?pagename=$matches[1]&page=$matches[2]"
}

Anything wrong in it?

UPDATE 2:

I found my error when using var_dump($wp);.

I got this response:

  ["query_string"]=>
  string(25) "statut-membre=sample-page"
  ["request"]=>
  string(11) "sample-page"
  ["matched_rule"]=>
  string(10) "([^/]+)/?$"
  ["matched_query"]=>
  string(25) "statut-membre=sample-page"
  ["did_permalink"]=>
  bool(true)

Wordpress was querying a taxonomy called statut-membre while looking for my pages. I noticed I had an empty rewrite slug('rewrite' => array('slug' => ''),) in that register_taxonomy function. I added a slug and resaved my permalink structure, now my I can access my pages.

Now the query looks fine too:

  ["query_string"]=>
  string(20) "pagename=sample-page"
  ["request"]=>
  string(11) "sample-page"
  ["matched_rule"]=>
  string(20) "(.?.+?)(/[0-9]+)?/?$"
  ["matched_query"]=>
  string(26) "pagename=sample-page&page="
  ["did_permalink"]=>
  bool(true)

Answer 1

can you try replace

RewriteRule . /cpu/index.php [L]

by

RewriteRule . /index.php [L]

as for a way to debug...

well you can always var_dump a $wp_query object to get an idea what variables not passed to wp. (you can place ) into first line of your header.php template.

and i belive next step will be debug of rewrites in this case usefull filter is rewrites_array_rules which you can use for debug proposes in a next way

add_filter('rewrite_rules_array', 'rewrite_rules_array_filter_debug', 10000);
    function rewrite_rules_array_filter_debug($rules){
    var_dump($rules);
    return $rules;
}

add this to header php

   <?php 
          global $wp;
          echo '<pre>';
          var_dump($wp);
          echo '</pre>';
   ?>

this shoudl give you a point what rewrite rulle trigger to you page request.

Answer 2

You would want to tell apache to follow your .htaccess file. You can do this by editing the apache.conf file

$sudo nano /etc/apache2/apache.conf

Scroll down to the line By default it will be:

<Directory /var/www/>
Options Indexes FollowSymLinks
AllowOverride None
Require all granted
</Directory>

change the value of AllowOverride to All so now it becomes:

<Directory /var/www/>
Options Indexes FollowSymLinks
AllowOverride All
Require all granted
</Directory>

Press ctrl+x and press y to save the configuration file. In order to make this changes to server first enable the mod_rewrite by.

$ sudo a2enmod rewrite

And then restart the server

$ sudo service apache2 restart

Done!

Source: https://www.wst.space/riddling-with-wordpress-permalink-setup-issues/