An erroneous CSS declaration caused this issue. The permalink section is not needed on a publication page, so it was removed to avoid confusion. Unfortunately, we were initially hiding it through CSS and that same declaration was hiding the permalink field for posts/pages/custom post types.
Actually, 2.1.0 released just after I wrote that 🙂 Let me know how it works for you.
The problem with the permalink section is that it’s a meta box that can’t be completely removed with remove_meta_box(). That function call removes it initially, but once the publication auto saves, it pops back in. So the CSS declaration was used to set the meta box to display:none; so it wouldn’t confuse users. I was just accidentally loading that CSS for every admin page rather than just the Add Publication page. Completely my fault.
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