Hmmm....well at least now you know she is not confused by the towel, she is just not associating the litter pan as her exclusive toilet. Maybe the sleeping towel should be put back, so that she stops sleeping in the box (She might be doing that since it is soft).
I would expand the quest for answers. See if there are any forum recommendations at www.rabbit.org and also try asking at the Etherbun group on Yahoo Groups. You need better advice than I can give. She IS still very young so do not lose heart, this can take time!