In https://github.com/RethinkRobotics/baxter_interface/pull/74/files#diff-393fafc5e38a00ca79cd9d500e6ab03cR367 , joint current positions are set to first trajectory point. And those positions are got from /robot/joint_states.
But when Baxter's hand grasps heavy object (or gripper is heavy), /robot/joint_states and commanded positions are very different. In that situation, Baxter's arm goes slightly down because first trajectory point is different from current commanded joint angles.