Did you see the Warning at the top of the Feedback Analysis doc, it was added about a week ago:
The feedback gain calculation assumes that there is no mechanical backlash, sensor noise, or phase lag in the sensor measurement. While these are reasonable assumptions in many situations, none of them are strictly true in practice. In particular, many “smart motor controllers” (such as the Talon SRX , Talon FX , and SparkMax ) have default settings that apply substantial low-pass filtering to their encoder velocity measurements, which introduces a significant amount of phase lag. This can cause the calculated gains for velocity loops to be unstable. To rectify this, either decrease the amount of filtering through the controller’s API, or reduce the magnitude of the PID gains - it has been found that shrinking gains by about a factor of 10 works well for most default filtering settings.