The controller from entvars_t has been changed from FIELD_INTEGER to the array of FIELD_CHARACTER in 89610a2
Now it's not handled in EntvarsKeyvalue thus the error message.
Setting the controller directly in the entity parameters had its uses, even though only the first value was read. The first controller sets the head turn for some monster models. E.g. in Opposing Force you could set controller to 127 on item_generic in order to create a non-solid corpse with head directing forward.