Try removing the shorting wires on the input pins(2,3,4) to the channel dedicated to the CJC. When you have the switches (S1-S6) set to use the CJC, you do not want any input wires on the terminals to Channel 0 - the switches take care of signal routing. As a note, make sure the switches (S1-S6) to enable the CJC are set to the same mode as the DAQ card (differential, single-ended) or additional measurement errors will result. I hope that this suggestion helps.