Nah. I think we've isolated the problems.
It sounds like noisy inputs to the DAQ board.
As I said, TCs are very prone to noise on the line, and normally there's a filter on the TC to eliminate the noise, and just get the DC component of the TC--but you don't have that.
Therefore, to get the same effect, you're going to have to average many readings, which will in effect average out the AC component.
Another thing--if your panel (TC junction) is in a controlled environment (same temperature all the time), I would average the CJC IC voltage, and just continuously use that, rather than reading it every iteration.
Try something like this attached file.
Mark