Sorry about not getting back to you.
Your data file has SRM chromatograms in it. Whenever a raw file has SRM chromatograms in it (specifically, whenever a raw file contains more than 2 chromatograms), Skyline will ignore all of the spectra.
In order to get Skyline to pay attention to the spectra, you would need to create a file which did not have any chromatograms in it.
One way to do that would be to use MSConvert to convert the raw file to .mzXML. Since .mzXML cannot contain chromatograms, the chromatograms would be removed.
There might be a better way to do this by maybe checking the "SIM as Spectra" checkbox in MSConvert.
If you send me your Skyline document I might be able to try some of these ideas out and give better suggestions.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files.
If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:
Sorry I do not have any good ideas at the moment. Maybe someone else on the Skyline support board can give you better suggestions.