Broken wordpress permalinks on pages only

Not sure when it happened but the custom permalinks for pages on my client’s WordPress site have broken. I can fix it by reverting back to the default permalinks and then using the custom permalinks, but they break again whenever my clients edits a page. Blog posts, archives, tags, categories, and custom post types permalinks all work fine, it’s only pages that 404 when using custom permalinks.

The site has an .htaccess file with 666 permissions with the following in the file:

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

It also has mod_rewrite enabled.

Using WordPress 3.1.3

It’s not the plugins because I have disabled all of them and the permalinks for pages still don’t work.

Please help.

Do you have a custom post type? This is exactly the kind of behavior you will see from have a custom post type with a slug that matches the slug of your pages. For example, if you have a page called “portfolio” and a post type called “portfolio”, both with a slug of “portfolio”, 404s are going to be thrown for some of these.