Are the CD's you're playing burned CDs or Mastered CDs?
If they are burned, are the songs that you burned in a lossless quality or MP3? If they are MP3's, then there's your problem---MP3 kills about 60% of the music quality every time you compress it, hence it just will not sound 'correct'.
Personally, for me, I'm super @n@l about sound quality which is why I always buy my music on a CD. (never from iTunes, or other subscription services) just simply because I don't like compressed music. When I rip the music to my computer, I always use either a WAV, FLAC, or some other lossless encoding to prevent the music from being compressed---But then again, that's just me.
What I'd suggest is, if the music that is being effected is MP3, find the CD that it came from and play back the original source (Mastered Material) as that's probably where your problem is coming from.
Hope this helps, and good luck!