Christoph:
I don't see how changing from the ADuM5401 to the ADuM6401 should change the noise on the inputs, since they are basically the same die, but with a thicker polyimide insulation on the ADuM6401. Are you using the same exact PC board? Can you share a section of your schematic and layout showing the ADuM6401 and input connections and bypass connections?
Regards, Brian