This is an old post, but I came across exactly the same problem with ACF 4.4.0. I have two relationship fields assigned to my normal WP posts.
One of the relationship fields displays a list of all WP posts and has no taxonomy restrictions. The posts appear as expected in the relationship selection area.
The other relationship field is supposed to display a list of custom post types restricted by a custom taxonomy. Nothing appears in this relationship selection area; it’s completely blank. The field itself appears, but the left pane is empty. Removing the taxonomy restriction did not fix the problem – the only way I could get anything to appear in the left pane was to choose either WP posts or WP pages as the post type.
This appears to be a bug, but considering the lack of similar reports (I have been unable to find much online), maybe it’s a unique situation.
I upgraded to 5.0 and that fixed the problem – kind of. The left pane correctly populates with the custom post type, but the search feature does not work. Regardless of what I enter, I get “no matches found”. I describe this problem in this related ticket:
http://support.advancedcustomfields.com/forums/topic/search-not-working-on-relationship-field-in-wordpress-4-0/#post-22436
So, upgrading to ACF 5.0 fixes the issue of the field not being populated, but now search does not work with custom post types.
