ADC Input Problem/Considerations
Its hard to tell without comparing your breadboard and the PCB version. Maybe the input track now has significantly more capacitance to ground? Can you lift the input pin and connect directly?

The signal generator will have a lower impedance output, and potentially a high power too. Its also possible that before you were seeing harmonics due to the breadboard which were not present in the input. Try a sine-wave frequency sweep with the sig-gen.

Standard practice is keep everything very short, decouple or screen everything that is not signal.