When Skyline extracts chromatograms from a raw file, Skyline looks at how many chromatograms the file contains in order to decide whether it is SRM or full scan.
If Skyline sees more than one chromatogram, then Skyline decides that it is an SRM file, and then Skyline does not look at any of the MS1 or MS2 scans that might be in the file.
I would recommend that you use msconvert to create a .mzXML file from your .raw file. The .mzXML file format cannot contain chromatograms, so Skyline will know to extract chromatograms from your MS2 scans.
Here is where you can learn more about msconvert:
I am attaching your .raw file converted to mzXML.