The problem is that when you build a plugin of other code to add fields that ACF will access that you’re not saving the reference value, see this page for more information: http://www.advancedcustomfields.com/resources/get_field_object/
Your choices are to build your code to also store the reference value or to use the standard WP get_post_meta() function. http://codex.wordpress.org/Function_Reference/get_post_meta
