Looks like you have the some time calibration, not sure if it's the correct one. Sample the sine wave from the calibration clock, once with and once without the timing calibration, then you will see if all points lie on a smooth line. Left: without timing calibration, right: with proper timing calibration:

If your points do not lie on a smooth line, you might habe a problem such as the wrong channel for calibration, an offset of 1 in the index of the time array or some other software bug. Measure the same signal with the DRSOsc application and then your code. If the results differ, you have a software problem on your side.

Stefan