The 100Hz modulation is likely caused by the bridge rectifier at the mains input of a SMPS. Because the diodes conduct only at the mains waveform's peaks, they act as switches that conduct switching noise.
there are no AC on board, I use 12v laptop-style SMPS. It works perfectly fine in terms of continuous operation without issues, I played Dreamcast using it for hours and hours.
there was found a decision on the internet, to use C or RC-circuit in parallel to IC feedback resistor.
that is called bootstrap capacitor if I am correct, and I have one for each switcher feedback as mentioned in datasheet. Mine is 1uF which is the best value which includes maximum performance (stability, noise cancellation) while being not near the upper limit.
However, if this analysis is correct, it may be coming from the 12v input wall charger itself.
Don't you think some extra input filter elec. caps can help here since it is low frequency?
Experience I have: I have low-noise DC-DC (with XL4016) with less then 1 mV RMS noise and I didn't use large ground pour. Design was made with wide printed wires which go somewhere near each other, more or less close to each other.
I am interested in this solution if you can explain more or post circuit or methods.
Big L values everywhere except main switcher L may worsen stability but not help. That's one of the reasons you are told not to use large L values.
For example, it you decide to add post-filter after switcher with large L - it will provoke instability. And similar things may happen with unlucky L before the switcher. A typical 'safe' post-filter L value may be no more than 10-20% of a main switcher L.
Right now I didn't add any but maybe a 1uH is good? assuming the main switcher L is 4.7uH.
That is for post-filter, but why also pre-filter?
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from my previous waveforms... how much is the actual ripple and noise figure is? how can we know it for sure without the oscillation?