Hello SCXI...
I am assuming that the problem you are referring to is displayed by the rapid oscillations in your pictures. From your description, it sounds like the problem may not even be hardware related, since you noted that the "target" value goes crazy also. I am assuming that this target value is defined completely in software. Is this true?
For troubleshooting purposes, it would be best if you could try to isolate whether the issue is hardware or software related. If it is practical to do so, try measuring your physical signal by another means for comparison. It looks like you are monitoring temperature. If you are using thermocouples, I know that the voltage generated is very small, but try to get a reading using a voltmeter or oscilloscope during your program's execution and see if these readings fluctuate also.
If you do see the same type of oscillation, consider whether or not you might have any noise sources such as motors nearby. It is possible that you could be picking up 60 Hz noise from somewhere. For more information on reducing noise, please refer to the tutorial
Field Wiring and Noise Considerations for Analog Signals.
Let us know if you are able to determine whether or not the actual signal is fluctuating, or if the disturbance is somehow software related.
Best regards,