Because the iTunes music player does not have tempo controls or a 'cut and fade' feature, I often do such editing in a wav editor and save as a new file which i can then play in iTunes. Those are the files which are problematic, although not all of them -- like I said, only some of the more recent ones. To get a fresh copy, I'd have to re-download the music file from iTunes, then re-edit it in my wave software app, a burdensome chore.
I'd note that last year, Apple put out a new iTunes version that no longer played certain file types. There were a lot of complaints on these forums about that amid denials by Apple that a problem existed, but they did eventually fix the software in a subsequent version. That's one of the reasons I think their updated iPod software has a bug in it -- and doubt they would admit it -- but I haven't seen others with this problem, have you?