This issue affects filter functionality when first item in fields list is a field from a related table (added by setRelation function). In this case, at the first time opening the filter window, value field is not avaiable.
I can reproduce the issue and I will try to fix that for the next version release. In any case I will inform this post.
At the meanwhile as a work-around if this is an important functionality for your CRUD and you can’t change the ordering of the fields then you also consider to add the below line:
$crud->fieldType('group', 'relational_native');
that will actually transform the searchable dropdown list into a native one.