When you say torque capacity, are you talking about holding torque? If so, it could be that your amplifier is slowly lowering the amount of current it supplies to the motors, since holding torque and current are related in stepper motors.
NI's Motion Controller only sends a pulse train to the amplifier, so the problem probably resides in the amplifier or the motors themselves.
If you have a National Instruments or NuLogic amplifier we can troubleshoot it further over the phone. Just go to www.ni.com/ask to set up a service request number.
Kyle V
Applications Engineer
National Instruments