I just got off the phone with the Sabre help desk. They say if the FF numbers are entered properly, there will not be a problem. Too often the person who enters the ff number will just enter the number using the basic entry code. For example the basic entry is FF(airline code)(FF number) - (passenger code). Sabre will accept numerous entries like this but will default to the first one in the list. The proper entry(in sabre) would be FF(the Airline code)(the FF number) / (the segment number) - (the passenger code[ie 1.1 or 1.2 or 2.1])

This seems like it would work.