FLAC is bit perfect and better than even Apple Lossless, which clips off HDCD suffixes and does other weird stuff. You can encode and decode between FLAC and AIFF an infinite number of times and you can prove they're the same file with a hash. FLAC requires some processing to use due to the way the container and codec works, though, which is why the old units couldn't deal with it in realtime. This doesn't mean Pioneer DJ has FLAC decoding working perfectly on their new units, but the OP hasn't actually done much to establish that's what's going on.