Sounds like you’ve got Preset code going down on a striped tape.
Re black the entire tape. Set deck to INT timecode / Preset / LTC and VITC.
Then when it’s finish set deck to INT timecode / Regen / LTC and VITC
Also what is your reference setup? Try setting deck to Input Video and make sure there’s not a signal loop going back to Kona. So Kona is plugged into deck and deck in NOT plugged into Kona.