SCXI-1125 overvoltage criterion

Hello all,
I am going to use a SCXI-1125 module with SCXI-1327 terminal block to condition thermocouple signal. Estimated signal range is about 0-50mV.
The problem is, since the thermocouple bead must be attached directly to a resistance heater, on which current flows at 100Hz with certain duty cycle, it is expected that part of the heating voltage(no more than 1V) will be imposed on the thermocouple bead. We can manage in LabVIEW so that no overlap exists between data acquisition and heating.
I use an oscilloscope to measure the voltage from the thermocouple wires. Surprisingly, at the end of each current pulse, there seems to be a negative peak voltage. The duration of the peak is about 0.02ms out of every period, which is 10ms. Magnitude of the peak varies between 1V to 20V.
I look into the manual of SCXI-1125, which says when measuring voltage larger than 5V the 100:1 attenuator on the terminal block (for example, SCXI-1327) should be applied. But when I tried this way, the temperature signal suffered from large noise, maybe due to its very low nature.
If I bypass the 100:1 attenuator, is there possibility to damage SCXI-1125? I wonder whether the peak voltage or the continuous voltage should be avoided. The manual doesn’t provide parameters such as “input current during overvoltage condition”.
Any suggestion would be greatly appreciated.
Su

Lynn,
Thank you for your very fast reply. In fact our heater was fed by two 12V lead-acid batteries in series and the averaged power input is ragulated by an IGBT module, and the two electrodes which stretches the heater are floating-connected rather than grounded. The thermocouple wires are also ungrounded.
During the run, I think there is no large external interference(such as a welding machine or other on/off operated device) nearby. Once I recharged the batteries beside the apparatus and interference as large as 1 V appeared. In other case no descernable random interference seems to exist.So maybe the problem is from the inner of our device?
The png file named "nonoverlap" shows the voltage signals every 50 samples for a period, during sampling no current flows. The png file named "temp" is the temperature signals corresponding to the previous voltage signals, every data is the result of the average value of the 50 samples mentioned above. The last file named "interactive" is the voltage signals every 150 samples in a period, with each last 100 samples overlapping with the heating pulse. You can see two peak signals in the beginning (the data before the first negtive peak come from a previous run).
Best regards,
Su
Attachments:
Nonoverlap.PNG ‏50 KB
Temp.PNG ‏31 KB
Interactive.PNG ‏35 KB

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