It is possible that each segment can have it's own fare class. Do you have your original booking e-mail or retrieve it from nwa.com? You will see the AF PNR code for that segment. With that you can look up what booking code AF was booked into to verify that you were suppose to receive the 50% EQM bonus.

http://www.nwa.com/worldperks/earn/a...html#airfrance