Hi Cueball,
Although you already received an answer through email support I thought I would post an answer here for anyone else who may have a similar question.
The drift in accuracy of the internal reference is corrected through a calibration factor which is updated during the external calibration process. The calibration procedures have been written to take a particular, accurate external voltage reference. The internal refterence is corrected, even if it is at a different level than the externally provided source. In the case of the M-Series calibration, a polynomial algorithm is used which facilitates accuracy at the full range of the card.
Regards,
Jennifer O.