I do not know the answer to your question but if you send us your Skyline document we can take a look.
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:
It might be helpful if you could send us two copies of your document: one where you applied the IM settings after adding the decoys, and the other one.
I am not exactly sure what you mean by "Apply the IM settings". There are certain things that you definitely should not do after adding the decoys (or, if you do them, you need to add the decoys again). When you use the "Add Decoys" menu item, Skyline gives you a list of peptides which have different masses, but share a lot of other characteristics such as (predicted retention time) with the target peptides that they were generated from. If you were to then do something to change the target peptides, and that same change was not applied equally to the decoys, then there would be a difference between the targets and decoys. If you were then to train a peak scoring model, the trained model might heavily weight a particular score because it happens to provide very good separation between the targets and the decoys, but that would not actually help the model distinguish between true and false peaks.
If we see your Skyline documents we will probably be able to tell you whether anything invalid has happened with the targets and decoys.