How to freeze NIOS2 during sensitive measurement?

Hi:

It seems like noise coupling from the digital power supply to the analog power supply (and grounds). It's a very common source of errors in mixed signal systems.

If you're sampling very slow signals like temperature, the problem could be solved using oversampling and filtering (FIR, IIR, average, etc.); but if high bandwidth analog signals are involved, the problem SHOULD be solved using careful PCB and decoupling design.

First of all, isolate the power supplys and grounds, use ferrite inductors for joining the analog and digital ground-planes. And, try not to pass along digital signals like clocks inside the analog circuits area.

Take into account something, there's a compromise relation between PCD size and crosstalk+noise coupling, the shorter the distance, the higher the coupling.