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 iTunes’ 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 tracks’ copy protection), those MP3 tracks won’t copy to an iPod. Try, and you’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.