It could be a matter of over-modulation, but from what you describe, I really doubt it. If they are .mp3 files you can adjust & compensate for this with a free program, MP3Gain. You can set whatever db level you want to be maximum. 89db is default but I think that’s a bit on the low side and set mine at 94db. Still most CD’s I rip are at a minimum of 97 to well over 100 resulting in severe clipping and distortion. The program adds the playback settings for the track into the ID3 tag that’s already there, so it doesn’t modify or change the file at all. Just the way that it’s played.
Have you tried re-ripping these affected tracks? You might also drop down to 256 kbps. It’s still high quality. It’s what I rip at in .mp3 format and I have no problems other than an occasional hiccup where I have to re-rip it.
One other thought, does this happen when the backlight goes off? If so, does it change and play normally if you move the scroll wheel and the backlight comes on? There was an issue like this that affected high bit-rate files, but that was supposed to have been fixed in the most recent firmware update.
Glad to see you got that giddiness under control. 
