I’m having the same problem with WP 3.6, ACF 4.2.1 and Flexible Content Field 1.0.2. I’ve tried creating a new flexible field with a relationship field inside it. After putting error_log(var_export($value, true)); into line 891 of core/fields/relationship.php I can see nothing in my error log wrong with the values that are being passed through the function — but no values are being saved.
