Buzzp,
Our situation here is that we have a beaded thermocouple connected to a National Instruments instrumentation chassis. The beaded end (i.e. the signal source end) is touching an internal surface of a pump we are testing. The pump is directly mounted to a 3 phase motor, in which the motor case is connected to ground.
When we connected the signal wires coming from the thermocouple to a hand held themocouple reader the reading we get is correct. However, when we connect the signal wires of the thermocouple to the computer instrumentation the signal biases up or down by a magnitute of 10 or more.
In addition, when we prevent the bead of the thermocouple from touching the metal pump case then both the hand held thermocouple reader and the instrumentation will read the correct temperature
The instrumentation is powered via a 115VAC outlet in the lab, which in turn happens to share the same netural and ground as the 3 phase power to the motor (this is done via a step down transformer).
Given that the hand held thermocouple reader is powered via a battery, thus it is inherently isolated, I thought that powering the instrumentation from an isolation transformer (or isolated power supply) would help removed the apparent ground loop that has formed. There is no shielding on the the thermocouple connection wire.