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I'm using a theme with custom taxonomies. I want to use corresponding archives. If I try the template out on one network it works, and on another the permalink will take me to 404. The only difference between the two networks that I know of is that the one that doesn't has domain mapping, courtesy of this plugin.

Ideas for how to fix it?

(Just for the sake of it, here is how I generate the archive links: )

<?php foreach( get_terms('region') as $region ): ?>
    <a href="<?php echo get_term_link($region); ?>"><?php echo $region->name; ?></a>
<?php endforeach; ?>
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Have you visited the Settings > Permalinks page? Visiting that page will flush and recreate the rewrite rules, and that may help... – mltsy Aug 28 '12 at 21:46
Also, can you describe the "code" you're trying out that's working on one network, but not the other? And give more information about the permalinks that you're trying to use? – mltsy Aug 28 '12 at 21:48
By "code" I mean the template I wrote, the only relevant part of which is how I generate the permalinks. I now include that in my post. Yes, I tried visiting that page and also updating the permalink settings, but it did not help. – Calle Aug 28 '12 at 22:09
OK, after a night I visited the permalink page again and things started working. Why on earth this it did not do it the first time I visited that page and even clicked save to try to update the permalink structure I don't know. But there was the problem. – Calle Aug 29 '12 at 6:34

It's not necessarily a fix, but you should be able to use the Rewrite Analyzer plugin to help you understand how WP is rewriting your links.

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