Check to see that the midi tracks aren't overlapping on channels, as this might cause the note-offs of one to act on the other.
Another possible solution lies in the voice killing controls of Kontakt. Is your CPU getting really taxed? Kontakt will being killing voices once its polyphony setting gets maxed or the CPU is strained. It stops earlier sounding notes so that later ones can be triggered. You can adjust these settings under the options menu.
Please let us know if either of these helps or if you can provide any more information.