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I'm setting up a new site on 3.4.1 and the Permalinks will not work.

I have deactivated all plugins and switched to TwentyEleven and they still fail.

I can see through outputting $wp_rewrite that the rules are being flushed when I chnage the structure, and .htaccess is being updated, but no matter what I do, I just get a 404 error.

I also notice that it doesn't matter what structure I use (excluding default), all links are in the format of the /%postname%/ structure.

Any suggestions of what else I can try? Thanks.

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Is there a valid .htaccess file in your site root? – TheDeadMedic Jul 6 '12 at 11:13
Yes, the .thaccess file is available and being updated when I change the Permalink structure. Have deleted and ensured that a new one can be created also, and that worked fine. – David Gard Jul 6 '12 at 11:21

Do you have any custom post types? Is there any chance that a page or post is using the same slug as a custom post type?

Also, does your home page work or is it a 404 for all pages?

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Thank you King Li, but this is sorted now. – David Gard Jul 6 '12 at 12:13
Ok that's good to hear anyway! – KingLiNoodles Jul 6 '12 at 12:21
up vote 0 down vote accepted

As I was always getting a server generated error, a friend of mine pointed out that this meant the .htaccess file was not even being read.

He advised checking the .conf file for the site, and sure enough, there was a typo in the <Directory /var/www/...> entry, meaning that the directory was not being read correctly when a user visited the site.

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