You can't use the SCC-TC modules within a dual stage configuration. I have linked a document below that includes which modules can be used within a dual stage configuration.
I believe you're right in thinking that it is a ground loop problem. Within the SCC-TC module, AISENSE is tied to AIGND of the DAQ device. Therefore, if you are connecting a ground referenced signal to the negative input of the SCC-TC module, you will be connecting the ground of the device with the ground of the DAQ device. This could definitely cause a ground loop. The SCC-TC user manual (linked below) shows this connection in figure 3.
Unfortunately, there isn't a way to use the SCC-TC series modules in differential mode. Our SCXI signal conditioning hardware can be used in different
ial mode, but the SCC signal conditioning hardware must be used in NRSE mode.
Which SCC Modules Can Be Cascaded or Used in Dual Stage Mode?
http://digital.ni.com/public.nsf/websearch/7B801B3C9E0B82A386256C25007640CA?OpenDocument
SCC-TC Series Thermocouple Input Modules User Guide
http://digital.ni.com/manuals.nsf/websearch/B0009EED5EC0D8B086256C020070CA12?OpenDocument&node=132100_US
Regards,
Todd D.