If you send us your Skyline document I would be able to give you an explanation of any differences that you might be seeing between any two versions of Skyline.
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 know that we have fixed some bugs which would happen if your normalization method was "Equalize Medians" or "Total Ion Current", but other than that I can't think of anything that might cause Skyline to get different R-squared values in the calibration curve if the underlying peak areas were the same.