Hello HaD,
When looking at a DC signal the accuracy is specified as ±(0.65% of Input + 8.0 mV) at the 10 V
pk-pk range. Also, the PXI-5122 could be measuring high frequency noise coming in from your input signal. If you look at the Fourier transform of the signal are there any high frequency spikes? If so, at what frequencies? Additional shielding on the input signal could take care of some of this noise.
If you are looking at DC signals another option would be to oversample and average the signals coming into your device, or use a lowpass filter in software to remove the high frequency noise.