Locomotor training using body weight support on a treadmill and manual assistance is a promising rehabilitation technique following neurological injuries, such as spinal cord injury (SCI) and stroke. Previous robots that automate this technique impose constraints on naturalistic walking due to their kinematic structure, and are typically operated in a stiff mode, limiting the ability of the patient or human trainer to influence the stepping pattern. We developed a pneumatic gait training robot that allows for a full range of natural motion of the legs and pelvis during treadmill walking, and provides compliant assistance. However, we observed an unexpected consequence of the devices compliance: unimpaired and SCI individuals invariably began walking out-of-phase with the device. Thus, the robot perturbed rather than assisted stepping. To address this problem, we developed a novel algorithm that synchronizes the device in real-time to the actual motion of the individual by sensing the state error and adjusting the replay timing to reduce this error. This paper describes data from experiments with individuals with SCI that demonstrate the effectiveness of the synchronization algorithm, and the potential of the device for relieving the trainers of strenuous work while maintaining naturalistic stepping.