I’m not sure if this is exactly related, but I’m experiencing something similar. On a page (among many) using a particular template with custom fields, I wish to hide one custom field. Using the screen options at the top of the edit screen, I uncheck the field and it goes away. Upon updating the page, the box remains unchecked yet the field remains visible.
Running WP 3.9.2 and ACF 4.3.8