If I import raw data into SkylineCmd.exe and use the --chromatogram-file option to export chromatograms to a tab delimited file, how are the peak areas calculated?

I had - perhaps erroneously - expected that the peak area would be the sum of the intensities for the ion in question. I am using a transition list that is already in the template file, which is looking only at MS1 data. However I found that if I take the intensities from the exported chromatogram file and sum up the intensities of just the window that is +/- 60 seconds of the most intense peak for the ion m/z in question, I often get a sum that far exceeds the area reported for the chromatogram.

Is the area calculated differently? I may have missed a tutorial that better describes how this is done; please feel free to refer me to the one I should review for this if so.

Thank you
Lee