Do you mean that, if the field has never been set for the user. In other words, the user was never edited to select any checkboxes rather than the user was edited and all boxes unchecked.
In this case ACF cannot find the field object because there is not association found between the field and the user. Try using the field key.
Instead of
$field = get_field_object('preferences','user_'.$current_user->ID);
try
$field = get_field_object('field_1245678'); // or whatever your field key is
