If you can spare $49 there is a
commercial tool found on this page:
http://www.videowatermarkfactory.com/order.htm[
^] which allows you to operate it in batch mode. You can download a trial version that will work for 15 days, so you can see if it meets your requirements. If the $49 aren't too much and if you'll be doing this on a regular basis you should look into this if it's good enough for you.
Disclaimer:
I never was nor am I in any way affiliated with above mentioned company.
Best Regards,
Manfred