I am assuming you are applying the low pass filter live with the scope running? Have not seen this issue and was not able to duplicate it here but I see the Pico team is on it as usual.
We do not normally use the filter live at all but rather apply the filter to the capture after the fact. This way you do not compromise your sample rates and can dial in just the desired amount to clean up the capture. This may work better for you.
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Pico Technology — automotive lab scopes and diagnostic equipment