Similar to the weird first-time-only bug I had with the stop button in the phrase editor, for my first time fidgeting with the Keyzones neither the dot on the keyboard indicating the root note nor the horizontal resize handles on the keyzones were present with a sample loaded in. I loaded multiple samples into an instrument, hit Distribute, and the handles appeared. I hit Layer and they went away. The vertical (velocity) handles were still present. I hit Distribute and Layer again with the same result. I deleted the instrument and loaded another couple samples into another instrument. Suddenly the handles were present regardless of whether I hit Distribute/Layer. I closed and restarted Renoise. Everything continued to work properly, and the root note dot is also present again.
Super weird.