Why is the MM orbital hitting harder? There is no skill points buffing OS damage for MM. MM orbital should do 15% less damage than engineering OS. Remember the PvP set bonus is removed so you get only 3 ticks not 4. So you need to change your calculation.
We were talking about damage per activation time. In the case of a marksman sniper, they get talents that reduce the activation time by 1 second. They also get 15 seconds off the cooldown (60-45 on live, 45-30 on PTS). So if its DPS when used on cooldown, marksman wins easily, and if its DPS per second of activation, Marksman wins.