Hi Steve,

The Thru track is probably sending the notes on a different channel than Kontakt is set to receive them.

By default, the Thru track is on MIDI channel 5, so it would work if you loaded the sound into the fifth slot in Kontakt

Alternately, load your sound into the first slot in the Kontakt interface, and select Forced MIDI Chan = 1 in the VST/DX Synths/Plugins window, so any notes sent to the Thru track are automatically rechanneled before reaching Kontakt.

Please let us know if that doesn't do the trick!

Cheers
Kent
PG Music