There is a VI if I remembered correctly that checks the the reading of the built in compensation. I believe it is called ACQ CJC Temperature.vi found in examples. It might be what you are looking for.
As far as the reading difference goes, there is an error from thermocouple to computer screen that you might want to keep in mind. The % error of the thermocouple, the % of reading error of PCI card and % error of SCXI module. All this error can be corrected with the VI though to compensate.
Staqnok