I just tested this on ACF 4.4.2 and WP 4.2.2, an it seems to be working for me.
Just curios if you also recently updated to WP 4.2 or later and if it stopped working at that point.
Do you have terms that are associated with this post type that are also in other taxonomies?
The reason that I ask is that in WP 4.2 shared taxonomy terms started getting split https://make.wordpress.org/core/2015/02/16/taxonomy-term-splitting-in-4-2-a-developer-guide/
