If plots are not lining up properly or appear to be different sizes, make sure the original plots are the same size. Open each plot and choose Plot > Set Plot Size. Verify that all of the plots have the same settings. You could also use one of the plots as a template when creating the others to make sure they are the exact same size.
KaleidaGraph is a thoughtfully designed graphing and data analysis application for research scientists, as well as for those in business and engineering fields. It produces publication-quality graphs, and easily converts the most complex data into a functional display.