With the dealer tool, or similar, you can go for a ride and record sensor values. It would be worth it to do so and see if the QS is sending the correct voltage to the ECU. If the QS is sending the right voltage, but the ECU is ignoring it, you would know it's not the QS.
If you disable the QS, and only use the clutch, does it shift normally?
That would tell you if its mechanical.
A shotgun guess, I think it's more electronic. I'd restore the tire calibration to default then test. If the problem persists, perform a tire calibration and test. If the problem persists again, you need to look at sensor values.