So let us break this down for clarity purposes:
- the NIN CD sounds poor when played over the speakers. (Multiple points of failure)
- other CD's sound good when played over the speakers. (eliminates most points)
- the NIN CD sounds good played via headphones.( eliminates most points)
If I have paraphrased this correctly, the headphones would bypass the amp output. I would find it difficult to say that the amp can't play a PARTICULAR CD without issue.
I would start by testing the CD on another system. I would also test with another set of speakers on your current system. It seems to be limited to that NIN CD, unless I have read your post incorrectly. Does a friend have a copy of this CD to listen to?
Your post title reads "clipping". This is not typically what clipping sounds like, and not at lower volumes. It could be damage down after severe clipping, but since other CD's sound fine, I would venture to say you have not clipped AND damaged the speakers.
