Updating to 5.5.8 – released today – seems to have fixed the issue, but answering anyway:
Registered users can create CPTs from a form on the front end. The line that attaches the custom field to the CPT is
update_field('field_561ef519ecce4', $_REQUEST['directory-link-source'], $post_id;
The site uses W3 Total Cache for caching but this problem happened when the plugin was disabled, however after I disable W3TC, I must disable ACF Pro before I am able to re-activate W3 TC.
I’ve spent way too much time on this issue to further nail down exactly what was going on. I’m just crossing my fingers. But if I can help solve a problem for someone else, I would be happy to to some tests to further isolate the problem.