Hi,
RailClone Colour should use the existing UVW mapping on the segments, so the only reason for this might be if the segments themselves were being deformed. Are you using RailClone's automatic Box Mapping features? If so maybe it's related to that. Would you mind uploading just the roof so we can take a closer look? If you're prefer no to upload it here, please feel free to send it to support@itoosoft.com.
Many thanks,
Paul