I have a few songs here and there that were either ripped before going to E.A.C./dbPoweramp/etc, or were too scratched to rip in said programs, and were done in iTunes.  It sounds like the CD is skipping, only you're listening to a digital file on your computer.   
Thats actually why I started using E.A.C. in the first place.  Way back when, iTunes would only do one pass at each track.  Hopefully they've wised up since then, but I dont know.