Unfortunately you do not show all your code.
The stripes are offset because they seem to have a different starting point. You must make sure that the datasources of both axes start at the same time. Maybe the first datapoint of one chartsource starts at, say, 9:00 and the other source starts at midnight. If both series go through the axis transformation then the 9:00 data point becomes 0 while the midnight data point becomes some negative fraction. Be caseful to apply the transformation correctly. To be more precise: I'd speculate that the first datapoint of the 9:00 series is "startdate + startime" (where starttime corresponds to 9:00), but the midnight data start at "startdate" only.
The "AChartSource.Add(days, days, s)" adds the number of days passed since the 1st data point ("days") as an x and y value to the chart source, along with the label "s". Using the days also for the y value, is not necessary, therefore, you can use "AChartSource.Add(days, 0, s)" (with 0 or any other value for y) as well. But maybe you want to rotate the chart (interchange x and y) sometimes in the future, hence I am inserting the value for y as well, and it does not cost anything. - It has nothing to do with the offset in time scales.