Can you send us your Skyline document? We can take a look.
In Skyline, you can use the menu item:
File > Share > (complete)
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.
If that .zip file is less than 50MB, you can attach it to this support request.
Otherwise, you can upload it here:
I am not sure I understand your question. If you post a screenshot, we also might be able to see what is going on.