CLA,
I believe the difference is related to "unintended couples" in the leads. Before I retired, almost seven years ago now, I was involved in engineering management for a large company. We used thermocouples in many applications. When we had questions about accuracy and unusual readings, it almost always came down to the leads.
Here is some technical information that might help:
http://www.picotech.com/applications/thermocouple.html
Thanks for all you do!
R2B