Can you send us your Skyline document?
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 also send us the .raw files that you are having trouble with.
The Share Document dialog gives you the option to include the .raw files in the .zip file. Alternatively, you could zip them up and send them to us separately.

Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
https://skyline.ms/files.url

After I see your files I will probably be able to tell you exactly what is going on.

There is some more information about using SureQuant with Skyline here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=TriggeredAcquisition

One problem that people sometimes run into with SureQuant is that the "Scan Description" has been set in a very specific way that causes Skyline to skip over spectra. There is some information about that here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=TriggeredAcquisition
-- Nick