No kidding! Chances are if you are reading this you’ve done some head scratching on this topic.I’m willing to bet the problem is you’ve changed somtheing in regards to your custom taxonomies and  a rewrite setting is persisting, thus pulling a 404, when you navigate to an archive page of said taxonomy(s). This was my problem.

Forst I tried adding the following to my functions files:

[code]
add_action(‘admin_init’, ‘flush_rewrite_rules’);
[/code]

…to no avail.

Then it was recommended I go into the wp_options table in your database and clear out the option_value field for option_name rewrite_rules. That option no longer exists.

Finally, I added /%tag%/ before /%category%/. Saved results and that worked – essentially flushing rewrite. Changed permalink settings back to /%category%/. Problem solved.