Hi piwdebar,
I noticed the burnout currents are enabled on the thermocouple channel. This will add some error so I suggest that these should be disabled.
You also used an external reference(1mA current and 2K resistor) as the reference for the thermocouple conversions. This is not a valid reference for the thermocouple measurements. I suggest you use the internal 1.17V reference fot these conversions. If the 1 mA current changes, this will cause an error for the thermocouple readings. However, the for PTC, both the voltage across the 2K resistor and the PTC will change by a similar amount when the external reference is used so, the change in the excitation current voltage does not affect the accuracy of the conversions.
Thanks and Best Regards,
Chris