iTunes mash-up?

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Just trying to track down a problem I’m encountering with iTunes, which may be SuperDuper related. I regularly sync my three hard drives. Once in a while I change my start-up disk. A few times now, after several sessions of syncing, my iTunes starts misbehaving: I click on a track, it refuses to play; it loses its album art; clicking on the actual file in the iTunes folder also fails to play the track. I’ve had to manually reimport 7500 tracks and album art from either my iPod or one of the other drives that by chance has a particular track still intact. Nobody at Apple Care had ever heard of this problem before. Once I’d got everything working again (I think) I erased one of my drives and cloned it from the drive that’s A-OK. Now I’m too inhibited to try Super Duper again, fearing the mad iTunes mash-up. Anybody encountered this weirdness?