For most of the "R" and "K" isotope modifications that Skyline knows about, there is one version of the modification which would apply to a particular amino acid regardless of where in the peptide sequence the amino acid appears, and there is another version which only applies to that amino acid when it is at the C-terminus.

For instance, there is a modification called "Label:13C(6)15N(4) (R)" and another one called "Label:13C(6)15N(4) (C-term R)".
You probably should have chosen the one that had "C-term" as part of its name.

If you want to learn more about working with modifications in Skyline you might find some useful information in this webinar:
http://skyline.ms/webinar10.url

If you are having trouble getting your Skyline document set up the way you want it, we might be able to help more if you could 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.

If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:
https://skyline.ms/files.url

If you want complete control over which residues have modifications on them, you can right-click on the peptide in the Targets tree and choose "Modify Peptide".
-- Nick