How to fix Magento CMS ignoring store view URL's?

We have 1 store with 2 views "us" and "uk" -- for the most part, all of the pages are the same except the uk version has maybe a dozen pages with different content.

When I go to mysite.com/uk/ it seems to work fine except all the links are done like this:

<a href="/.../.../">link</a>

So whenever you "switch" to the "uk" view... any time you click on a link, you're basically back in the US version.

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Is there a fix for this?

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The fix for this is to do it differently. Personally I would not use store codes to set the store view as you don't want your US customers looking at UK prices (and vice-versa).

You can use Geo-IP in your index.php to set the website code to uk or us. This auto-switch also makes your store better for not having 'duplicate content' and URL's that can be used anywhere, e.g. http://www.example.com/uk/mac/guffin.html won't load ideally in the U.S. whereas without the storecode it will.