I would fight this on principle alone and appeal it. It is not just the $800 and the 100S, it is the $800 and the 100S every year.
Did the FTB reject solely for having one employee that earned less than $57,000? If that is the case, I think an appeal would be relatively easy. I deal with the FTB a lot and they do make mistakes and give out incorrect advice. In recent years they have been issuing penalties for all sorts of minor things which don't exist and because the amoutns are low - usually less than $200, most people dont want to bother fighhting it and just pay up.