Is your target under effects that reduce damage resistance? Such as Attack Pattern Beta or Sensor Scan?
Are you hitting things like Engineering Team or Engineering Fleet that boosts certain skills for the duration -- these could be boosting your Eject Warp Plasma damage as they increase general skills tied to the power.
Engineering Team should add a few points to Engineering Training which adds some to Eject Warp Plasma. Not much, but every little bit could help. I usually save my Engineering Team for repairing hull damage though.