I finished converting a regular, old WordPress site into Multisite, and everything was working great EXCEPT for my custom taxonomies! Ugh! I tried a number of things, and then stumbled upon this comment on Jeff Sebring’s blog.

1. Set the permalinks structure back to Default on this page:

/wp-admin/options-permalink.php

2. Save Changes

3. Manually enter new permalink structure on this page:

/wp-admin/network/site-settings.php?id=1

Example: /news/%year%/%monthnum%/%day%/%postname%

4. Save Changes

5. Test links

Note: You’ll have to do this for each sub-site you have set up (id=2, id=3, etc).

Thank you very much!