Can you send us your Skyline document and .raw file?
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 .raw file are less than 50MB you can attach them to this support request.
You can upload larger files here:
I see that on the Full Scan tab of the Transition Settings dialog, you have "Isolation Scheme" set to "All Ions". You should probably change that to "Results Only".
"All Ions" is intended to be used with Waters MSe data, where there was no isolation window and everything got fragmented at the same time.
"Results Only" tells Skyline to trust whatever the mass spectrometer said the isolation window was.
After I see your Skyline document and .raw file I will probably be able to figure out exactly what is going wrong.