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Calibration mode differs from in VI collection

I am using a SCXI-1100 module for data collection within a VI.  I would like to measure the voltage across a shunt resistor and I need to know the voltage with precision of a tenth of a milivolt or better. 

 

In order to measure the voltage accurately, I have been performing the manual calibration that I can access through the DAQ assistant under callibration.  In this callibration mode, the module performs well.  The data collected for callibration matches within 00.02 mV with the callibration standard, however when I finish the callibraiton and try to get voltage measurements in the VI, the system performs poorly with a consistent offset of about 0.5 mV. 

 

Is there a reason that the data collected in calibration mode does not match the data collected in the VI?  When I've run the calibraiton, I've used the same settings as I run the data acuisisiton at in terms of number of points and frequency of data collection.  I could ap

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Perhaps because calibration applies only to the task that you've selected and does not carry across to other physical channels. Are you measuring from different tasks or channels that you did not calibrate?

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