Mainly happens with mp3s that I bought from eMusic
I've had this issue for a year now. The bulk of the songs that re-copy each time are mp3s that I bought off of eMusic or Amazon. The exceptions? One that I ripped myself (only one song - the other songs off the same CD don't re-copy), and two songs that I originally bought from iTunes as Protected files, then upgraded to Purchased; I kept both copies of the file, but now I'm deleting the Protected versions from iTunes to see how that works. I'm re-ripping the CD, but I notice that the CD came with a free mp3 download, yet oddly that's not the song affected by this, it's one of the iTunes AAC files.
I have a bunch of songs from eMusic and Amazon, but the bulk aren't affected by this problem. But the bulk of songs affected are from eMusic or Amazon.
After deleting the two Protected songs, the two Purchased songs are still re-copying.