If you send us your Skyline document as well as your .wiff and .wiff.scan files we will be able to figure out what is going wrong.
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.
If that .zip file and your .wiff and .wiff.scan files are less than 50MB you can attach them to this support request. Otherwise, you can zip them all up together and upload them here:
https://skyline.ms/files.url
-- Nick