Correct, I did get full miles ( just not the 50% extra status miles promotion). The Lufthansa agent told me though that he can;t guarantee that I would get 100% miles (luckily I did) for this LH flight, it will depend on Lufthansa and Aeroplan?

I already have given up on this 50% extra Status miles for this flight, my question now is how to avoid this situation in the future? Next time this happens and I only get half the miles? with the new TATL Tango fares coming up it will get even harder to make top tier and getting 1-2 IROP without full mileage credit will make it that much harder...