Unless the storage media develop errors, digital formats do not degrade with storage or repeated copying – unless you are decoding and then re-encoding the files using a lossy compression algorithm.
What you are experiencing is almost certainly a perceptual illusion.
Certainly I find that MP3s once decompressed, burned to CD and played on a decent stereo don't sound so good. This is undoubtedly due to the fact that a decent sound system shows up their flaws in comparison to normal CD formats.
The only software related explanation I can think of is decoding/re-encoding. What audio software are you using? I suppose it is conceivable that if you used some sort of editing suite to listen to tracks then they could get decompressed to WAV format only to be recompressed to MP3 format and saved like this when closed. Since MP3 (like JPEG and MPEG-2) is a lossy compression system repeated cycles would undoubtedly degrade quality – but I find it hard to believe that anyone could be doing this by accident.