WooCommerce Memberships is to blame for this. They have a function that removes ALL metaboxes from any other plugins.
The issue only arose recently because ACF used to force metaboxes to appear, but now is more compliant with best practices.
To fix this problem, SkyVerge (WooCommerce Memberships developers) have provided the following code snippet: https://github.com/skyverge/wc-plugins-snippets/blob/master/woocommerce-memberships/admin/acf-compat-add-field-groups.php
It can be put in your functions.php file or implemented using a free plugin called “Code Snippets”. The function basically allows ACF metabozes/field groups to appear on WooCommerce Membership related post types (e.g. single user memberships and/or membership plans).
