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:
2. Save Changes
3. Manually enter new permalink structure on this page:
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!