Can you send us your Skyline document and one of your Waters .raw files?
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.
You should also send us your Waters raw data. I believe that means that you should zip up one of your .raw directories and send that to us.
You can upload those .zip files here:
When Skyline extracts chromatograms, Skyline remembers the "spectrum identifier" of each spectrum. Skyline represents these spectrum identifiers as a short list of numbers separated by dots. If Skyline is unable to show you some spectra, it might mean that the spectrum identifier that Skyline saved with the chromatogram is incorrect, or for some other reason, cannot be used to find the spectrum that Skyline is trying to show you.
We will be able to figure out what is going wrong when we see your files.