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. If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:
I would expect that "Normalized Area" to have the numbers you want in it. I am not sure what might be going wrong but I will be able to figure it out after I see your document.
The "Area Normalized" column is not a useful column. It was added to Skyline a long time ago and is only available for backwards compatibility reasons and is calculated by dividing the transition area by the sum of the areas for all the precursors in the document which is very different from the number you want.