One thing that might be going on is that your settings are telling Skyline to only extract chromatograms within a certain distance of the predicted retention time.
You should go to:
Settings > Transition Settings > Full Scan
and at the bottom there is the "Retention time filtering" setting. You might need to change that to "Include all matching scans"
Other than that, I am not sure what is going wrong. You should send us your Skyline document and one of your 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 whatever chromatograms have been extracted.
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: