I agree with Ben, the test panels in MAX scan only one channel at a time while VI logger is scanning all selected channels. You might be seeing the effect of residual charge in the multiplexer as it switches through the different signals, specially affecting the lower voltage signals like the thermocouples and, depending on the measured frequency, the frequency inputs. Logging at slower speed may vary the results, pointing to this possible cause.
Try logging the data from the thermocouples only to see if there's still an offset. Try slower scan rates, and logging each channel individually to try to see if the problem is related to speed or just the scan order. This will help find the problem and then we can suggest some solutions.
Alejandro Asenjo
Nat
ional Instruments