I do not know the answer to your question but if you send us your files we can 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.
You should send us that zip file and one or more of your raw files.
Files which are less than 50MB can be attached to this support request.
You can upload larger files here:
If you hover your mouse over a chromatogram graph in Skyline, a dot shows up. If you click on that dot, Skyline brings up a window which shows you the spectrum, and you can see the m/z channel over which Skyline summed the intensities when extracting the chromatogram. Sometimes there really is no signal in the channel that Skyline summed across.
You can control the width of that m/z channel with the instrument and resolution or mass accuracy settings at Settings > Transition Settings > Full Scan.