I have never heard anything about avoiding cysteines for quantification. (There might be a valid reason for this, but I have never heard it mentioned). In the experiments that we do in our lab, we nearly always treat the samples with carbamidomethyl so that the cysteines to not for disulfide bonds with each other.
The reason to avoid things like missed cleavages and oxidizable methionines is that you may observe a change in the quantity of such a variant, but it will have been caused by a change in sample prep, and not reflective of an interesting biological condition.
If you would like, you could send us your Skyline document and we could tell you whether anything looks suspicious.
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. Otherwise, you can upload it here: