If you have specified the "Explicit Retention Time" for your molecules in Skyline, you should make sure that that time is within the time over which the SRM chromatogram was collected. If the Explicit Retention Time is not within the time range of a chromatogram then Skyline will assume that the chromatogram was not intended for that molecule.
If you would like, you could send us your .wiff file (and the .wiff.scan that goes with it) and maybe the .mzML file too and we can figure out why the chromatograms are not showing up.
Files which are less than 50MB can be attached to this support request. You can upload larger files here: