BW Variables not showing up in universe based on BEX query

We've been trying to create BO Universes on BEx Queries. When we create the connection, it reads the query into the Universe, however, it does not always read all of the BW variables associated with the queries. We've moved all filters in the BEx Query into Free Characteristics but BO Designer still does not read them into the universe or create them as mandatory filters in the universes as the documentation states. Any assistance is appreciated. Thanks