Is the thermocouple reading correct without the other voltage signal connected? If so, then you might be running into cross-talk between channels. I would check the source impedances of your signals and see if decreasing the scan rate of your acquisition helps the problem. I have linked multiple documents below that discuss cross-talk (charge injection) and possible solutions to this problem. I hope this helps.
Data Acquisition: Troubleshooting Unexpected Voltages or Cross-talk in Analog Input Channels
http://digital.ni.com/public.nsf/websearch/B9BCDFD960C06B9186256A37007490CD?OpenDocument
Is Your Data Inaccurate Because of Instrumentation Amplifier Settling Time?
http://zone.ni.com/devzone/conceptd.nsf/webmain/B9B5D37A04C772B58625686500695C20?opendocument
How Do I Create a Buffer to Decrease the Source Impedance of My Analog Input Signal?
http://digital.ni.com/public.nsf/websearch/CF83426BC3AC514A86256C10005A4771?OpenDocument
Regards,
Todd D.