Hi Kelly do you have a zip of 0.9.5? I would really like to get mine working again 🙂
I downloaded mine from here
https://downloads.wordpress.org/plugin/custom-post-type-ui.0.9.5.zip
Courtesy of the plugin developer – thank you!
From my experience with first-hand helping, just re-associating the post types/taxonomies and hitting save has actually fixed the issue. Doesn’t help me figure out why it’s a setting that gets lost in the first place, but it solves the issue on individual user ends.
Just to confirm Mr. Beckwith’s reply, I just upgraded to 1.0.4 today and none of the permalinks for my custom post types were working (“Page not found” error). However various data within the posts were still visible in other parts of the site (Featured Image, etc.). So I figured it must be some way the CPTs were being stored and synced in the db that had to be reinitialized. All you need to do is go under “CPT UI > Add/Edit Post Types > Edit Post Types,” then select each existing post type from the drop down and click “Edit Post Type” (but don’t alter anything!). As I said I think this just “reinitializes” or “reserializes” the CPT data the db after this latest version update. Your posts should start working again… at least mine did. Hope this helps.
Wish these settings converted more cleanly than they seem to have for a lot of people, but good to know that this step still works for some.