Just to be clear… do you mean MIDI Channels, or MIDI Tracks?
If you duplicate the MIDI Tracks, then the duplicates all respond on the same MIDI Channel (and will therefore all receive the same incoming MIDI data).
If you want independence between them, then you need to send each (duplicated) MIDI Track either to its own instance of the instrument, or if the instrument is multitimbral (such as Kontakt 5, for example), then at least set each track to a different MIDI Channel, and load up the same preset to each of those channel slots in Kontakt.