Hello,
Are you using the :AUTODETECT CVBS IN NTSC/PAL/SECAM, 8-Bit 422 encoder: script from the latest recommended script file (ADV7181C_ADV7181C@_ADV7341-VER.3.2c.txt) available here?
Are you using an ADV7181C evaluation board or are you using your own system?
Could you provide more details with respect to your statement "the hardware output HS and VS sync pins do not seem to work properly"? Does this mean you are probing the HS and VS output pins, you are not seeing any signal at all? Or does this mean that the timing or polarity does not correspond to the the requirements of your back end device?
If your issue corresponds to the latter, section 8.15 SDP Synchronization Output Signals of the ADV7181C Datasheet Manual Rev. C (also available here) will provide you with details on how to adjust the output HS and VS signals.
Best regards