In the Transition List that you give to Skyline, your light and heavy things should have the same Molecule Name, but there should be another column "Label Type" which is either "light" or "heavy" depending on whether the transition belongs to the light or heavy precursor.
In your screenshot, you have separate Molecules, and each of those molecules has one Precursor which Skyline treats as being "light".
In order for "Ratio to Heavy" to work, your Molecules need to have two Precursors, where one Precursor is "light" and one Precursor is "heavy".
Hope this helps. If you are still having trouble, you should send us your .sky.zip file.
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.
If that .zip file is less than 50MB you can attach it to this support request.
You can upload larger files here: