Can you 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 including extracted chromatograms.

You can upload that .zip file here:
http://skyline.ms/files.url

It looks like you might have added the heavy precursors after you imported results.

If you add anything to the tree of Targets in Skyline, you need to do:
Edit > Manage Results > Reimport
in order for Skyline to generate chromatograms for the newly added items.

If that's not what the problem is, then I would need to see take a look at one of the .raw files. You can upload your .raw files to the same place:
http://skyline.ms/files.url

(but, this really looks like you just need to do a "reimport")

Thanks Nick. It works but it looks like I have reversed results, for example, the heavy label is supposed to higher than light label, isn't it? Please see the attachment. Or which columns should I add to compare the "Heavy to Light" ratio while making the report template? Peak area? Thanks

In that screenshot, those columns that have "+/-" in their values the are from the "Precursor Result Summary". You probably don't want those columns. They are showing you the average across all of the replicates.
The columns you want are just under "Precursor Results" (not summary).

That other column that you have "RatioLightToHeavy" looks like the correct column. In the first row, it says that the light peptide is 74 times more intense than the heavy. Do you have some reason to believe that that ratio is incorrect?

You might want to take a look at the custom reports tutorial to learn more about the Document Grid:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

Thank you. I am trying to figure out how the "RatioLightToHeavy" comes from, for example, Total Area (light/heavy)?
Also, if there are some duplicates and how to determine this "RatioLightToHeavy"? Thank you.

The Total Area Ratio in a Precursor Result is the sum of that transition's peak areas divided by the transition peak areas of the internal standard precursor in the same peptide.
You might find that the "Ratio To Standard" column which is on the "Peptide Result" is a little more useful.
If a peptide has only one light precursor and one heavy precursor, then the Peptide Result's "Ratio To Standard" will be the same as the light precursor's "Total Area Ratio".
But, if the peptide has multiple light and heavy precursors (e.g. multiple charge states) then the Peptide Result's "Ratio To Standard" will be calculated based on the sum of the transition areas across those two charge states.

Another thing you might want to do is go into:
Settings > Peptide Settings > Quantification
and change the "Normalization Method" to "Ratio To Heavy".
Then, you can use the "Normalized Area" column (it's under "Peptide Result > Quantification > Normalized Area").

If you want to compare peptide abundances between your case and control groups, then you should take a look at the Grouped Studies tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_grouped