I cannot tell from your screenshots whether anything is going wrong, but if you send us your Skyline document and raw files we can always take a look.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms. The "Share Skyline Document" dialog also has the option to include the results files, which you can use, or you could separately package up the .wiff (or .wiff2) and .wiff.scan files.
Files which are less than 50MB can be attached to this support request. You can upload larger files here:
https://skyline.ms/files.url
The "Full Scan" graph in Skyline was only really intended for diagnosing problems with the chromatogram extraction. You cannot get much data out of that full scan graph. If you are interested in looking at spectra, there are probably other tools that are better for that than Skyline, including perhaps some tools that came with your Sciex instrument.
By the way, if you are interested in exporting lists of numbers from Skyline such as chromatogram peak areas, you should take a look at the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports
If you are interested in working with calibration curves in Skyline, I would recommend the Absolute Quantification tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_absolute_quant
If you are interested in comparing peak areas between groups of replicates (e.g. Healthy & Diseased), you should look at the Group Comparison tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_grouped
-- Nick
-- Nick