The pictures you posted look as expected and suggest your Nano works just fine. Apart form this, your question is more of a guessing game:
- Are you suggesting that the firmware works for V1 hardware only?
- Are you suggesting that your Nano is working better with the stock firmware?
- What is the nature of the noise and how is this different from what you expect?
- What do you measure and how do you take these measurements?
- How can you be certain that the noise is not part of your input signal?
If you think this issue is specific to the 3.4x firmware, posting in this thread is fine. If it is a general question on best practice for noise elimination, it may be more appropriate to create a new topic. In any case you need to explain in detail what the nature of the problem is or else no one will be able to give you meaningful replies.