Whoa. This is waaay too suspicious to pass off as a bug without quite a bit more information (from Chris Breen at Macworld.com):

Yesterday, I noted that iTunes 7.2 had trouble syncing certain MP3 files to an iPod. It appears that this is a bug.

Specifically, if you burn a playlist of iTunesโ€™ protected music to a CD in iTunes 7.2 and then rip that CD in the MP3 format (a trick people often use to remove the tracksโ€™ copy protection), those MP3 tracks wonโ€™t copy to an iPod. Try, and youโ€™ll be told that the tracks are incompatible with the iPod.


Chris goes on to show how rebuilding/recreating an iTunes library (the xml file keeping track of your stuff in lieu of a dbms) can get around this "bug." For me, in light of Sony's rootkit, you'll need a decent amount more proof -- here, what changes in the rebuilt xml that allows copying the burned CDs -- before I'd feel comfortable deciding this is an innocuous move in Apple's account.