I had a similar problem when listening to cd’s through line in on my Rotel CD14. With mine it wasn’t all cd’s. I think it was cd’s that were “louder” if that makes sense, remastered cd’s vs a disc from years ago. Anyways after much frustration I stumbled onto a fix. Try Audio Input - Line-in Input Resolution and try changing bit depth to 24 bits. This solved my issue, maybe it will work for you too.