Hi,
The pixel is an image measurement, whereas an arcsecond is a sky measurement. For example you might find that the graph shows a difference of 3 pixels, which is not much, but translated to arcseconds will show a more pronounced difference in the graph. It really is just the scale. The same is true when doing autoguiding, I use PHD, and in the pixel scale I am getting is 0.5 pixels up or down, but when looking at arcseconds the graph has more variation so I can adjust or fine-tune the graph to get a flatter line. ( I hope this makes sense).
Look up
John