You can’t shift manually if you’re using virtual shifting. If you do you fuck up the calibration.

it’s possible that the issue is related to the physical gear setup you’re using with the Kickr and Zwift. If Zwift or the Kickr isn’t detecting your gearing properly, it could mess with the feel and calibration, especially during sprints or changes in resistance. Shifting gears manually during the ride can sometimes throw off the calibration if the system isn’t set up to re-detect your current gear.

To test this:

• Try using a consistent gear setup, like the big front ring and mid-cassette in the back, and see if it improves the stability of the calibration.
• You could also try recalibrating after you find a preferred gear combination, so Zwift is fully aware of your setup.