Hello Rachel – Fantastic plug-in, but bad news I’m afraid as I think I’m having a related issue.
Its on a site that’s due to go live on Sunday, so is in the last stages of dev.
By default wordpress category pages (category.php) also show posts from child categories, which is exactly what I want.
I created a CTP-taxonomy with your plug-in and for a few days thought everything was fine. Now noticed that posts from any NEW categories (created after installing CPT-onomies) do not show up on a parent category.php page. However posts from child-categories created before creating the CPT-onomy still display as expected. The archive sole for a child cat still works fine.
Removed most stuff from functions.php and disabled plugins until I stumbled on CPT-onomies as the culprit. If I deactivate the child-category, posts come back on the parent category page.
Removing just the CPT-onomy doesn’t fix it, the posts only come back if I disable the plugin completely.
For what it’s worth, the parent cats and sub cats that are affected are the standard wordpress Post type. There’s no CTP-onomy or custom Taxonomy attached to them at all.
Happy to help troubleshoot where I can.
Thanks
Stef
edit: PS ran the snippet you suggested above but there’s only the standard taxonomies listed
Array
(
[0] => category
[1] => nav_menu
[2] => post_format
[3] => post_tag
)