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I would begin troubleshooting by verifying that you are inputing the signals which you are expecting. You can verify this using the test panels in Measurement and Automation Explorer (MAX). This offers the most direct interaction with the driver.
In MAX, simply right-click on your data acquisition board under "Devices and Interfaces" and select "Test Panels". Then enter the proper SCXI channel string into the channel input. Verify that the voltage signal being input is valid. If not, then you will know to check the configuration of your equipment in MAX and the physical connection of the thermocouple.
If it is valid, you could try some of the CVI thermocouple example programs on this web site. You can search through the examples from http://www.ni.com/ support under Option 3.
