Can you send us your Skyline document? I will try to figure out how Skyline came up with the times that it chose.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including spectral libraries and extracted chromatograms.
If that .zip file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here:
When Skyline is deciding what retention time to use for a particular peptide in a particular replicate, Skyline does something a little different if the replicate's name matches the name of one of the source files in your spectral library. However, if you're saying that your library was built from only one run, I cannot think of a reason you would be seeing the behavior you are seeing.