Without seeing the details of your whole system and the calibrator which you are using, my best guess is that the analogue inputs are responding to the different common-mode voltages in the two set-ups.
What I suggest is that you try calibrating again, using both pasive and active modes, and in each mode measure the voltage between the "transmitter" connections at P4 (difficult to read on the schematic) and analogue ground (AGND).
If those voltages are different, rearrange your connections to make them the same, and then try calibrating again.
Also, if you have unused inputs, dont let them "float", connect them to AGND.
I have seen this cause some very strange effects on systems I have worked on in the past.
JimB