I am not sure I understand what are saying that you did or what you were hoping to see.
When you set the Isolation Scheme to "All Ions", that tells Skyline that the chromatogram for a particular transition should be extracted from every MS2 spectrum, regardless of what the mass spectrometer said was isolated in that MS2 spectrum.
The "All Ions" setting is supposed to be used with Waters MSe data.
If you use the "All Ions" setting on data which is not MSe, then you would expect that the extracted chromatogram would be spiky like in your "Before correcting transition setting" screenshot, because some of the spectra had an actual isolation window that contained your compound of interest, and other spectra did not, and would be therefore expected to have much lower signal.
It sounds like you are saying that when you switched it to MSe, the spikiness disappeared, which is a little bit unexpected.
When you are trying to decide whether a chromatogram is spiky, you should make sure to use the menu item "View > Transform > None".
Sometimes, when "View > Transform > Interpolated" is selected, the chromatogram happens to look smooth even though the actual chromatogram that was extracted was very spiky.
Can you send us your Skyline document and some of your .raw files? We will be able to give you a better description of what is going on.
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 and/or your raw files are less than 50MB you can attach them to this support request.
You can upload larger files here: