Granted I do not have any experience with NI-DAQ devices but I do use thermocouples and other devices for reading them.
When I see someone using a DAQ for thermocouples my first question is:
How are you handling Cold Junction Compensation?
Most devices designed for reading thermocouples have an internal cold junction reference, most DAQ device do not.
Also remember that when reading thermocouples you are measuring millivolts/degree, that puts the DAQ in a very low voltage range and will be very sensitive to any noise. Possibly some measurement integration would help with this but most tiem noise needs to be dealt with on the hardware level. Like grounding all unused inputs of the DAQ to start with...