If I understand your problem correctly, this is a limitation of families that are hosted by specific elements (ceilings, walls, floor, etc...). Families that were defined based on such a template will not recognize elements in linked files. In order to have your families recognize elements in linked files, the families must have been defined based on a "face based" template, such as "Generic Model face based.rft". "ceiling based" families will not recognize elements in linked files.