The USB to Serial reference design isn't guaranteed to work with all RS-232 devices. Many RS-232 devices were developed to use the 9 signals in their own proprietary ways. Some RS-232 devices can also have certain timing requirements in their startup or initialization sequence.
This USB to Serial design was developed under the assumption that the 9 signal lines will be used as defined by the TIA/EIA-232 standard. Any special requirements of the 9 signal lines will require USB to Serial firmware modifications.