I think I just figured out what the potential issue is. The final Feature Class to Feature Class is going from a Coverage to a Shapefile. Not a problem in general, however, there are often field name issues when transferring data from a coverage to a shapefile (and reverse). For example, field names that are OK in one file type are not OK in the other due to the differing restricted characters, allowed field lengths, etc. This can cause data to not transfer correctly.