Thank you for sending those files.
There are a couple of things going wrong here.
1. Skyline has a bug where if you include the "Quantification" column in your report, then the pivoting will not work, and everything will appear on separate rows. This is because whenever Skyline compares two values from the Quantification column, Skyline always thinks that they are different, and must appear in separate rows. I will fix this in an upcoming release of Skyline-Daily.
2. Your report includes the "Area" column, which comes from the Transition Result. When Skyline is showing any columns from the Transition, and pivoting on the Isotope Label, Skyline has to figure out which light transition is the same as which heavy transition. In order to figure this out, Skyline looks at the value in a column called "Fragment Ion". This works great for peptides, since the fragment ion ends up being something like "y7". For small molecules, it ends up being something different (e.g. "Ion [166.050549/166.050549]") that in your case never is the same between light and heavy, so your light and heavy transitions end up on different rows. One way that you could work around this would be to give each of the transitions in your document a Name, but that's probably not worth the effort.
The other thing that you could do is remove the "Area" column from your report, and use the "Total Area" column instead.
When Skyline sees that you have no longer selected any columns from the "Transition", Skyline will stop looking at what appears in the "Fragment Ion" column. (There's another bug that as long as that "Pivot Isotope Label" thing is checked, Skyline won't notice that you've removed all the Transition columns, so you actually have to uncheck that checkbox and only recheck it after you have removed the Area column).
Here's what you should do to fix your report:
1. Edit Report
2. Uncheck "Pivot Isotope Label"
3. Remove the "Quantification" and "Area" columns.
4. Add the "Total Area" column (it's under "Molecule Lists > Molecules > Precursors > Precursor Results".
5. Check "Pivot Isotope Label".
Thank you for reporting these issues. I will try to fix them.
By the way, if you would like to do more complicated pivoting and would like more control over how rows are grouped, you should take a look at the Pivot Editor feature.
There is a PowerPoint showing how to use the Pivot Editor here: