Can you send us your files?
In Skyline, you can use the menu item:
File > Share > (complete)
to create a .zip file and supporting files, including extracted chromatograms.
You can upload that .zip file here:
https://skyline.ms/files.url
You should send us that .zip file as well as one of your .wiff files, and the .wiff.scan that goes along with it.
My guess is that this has something to do with your settings in:
Settings > Transition Settings > Full Scan
but it will be easier for us to figure out what is going wrong when we see your files.