Yeah sounds like the encoder might have been at fault but again I used the same converted files on the iPod and no problems there so really makes me wonder.
The scanning problem with the new file system is somewhat better and almost makes scanning issues a thing of the past but it still has it's initialization issues as reported earlier on the post. The progress bar is such a relief but you'll definitively complain about gapless in this version. I listen to Trance with 1.2.6 and to be honest I prefer the transition, in majority of EDM set transitions xfading is a common technique and really find the transition rather smooth. But it's me and I certainly prefer cross fading than one second transition delay that truly annoys me.
You're files, were they ripped directly with iTunes from CD or downloaded from the iTunes Store? If so You might want to try doing a complete tag strip of your files using MP3Tag an see if that helps. The only other option would be to dump the files and start from scratch and rip from CD using another ripper. My stuff was all ripped in 16 bit from CD or converted from HDTracks FLAC 24 bit using iTunes and it works fine. Not really sure what might be going on with your files. If it's a codec issue or a gapless playback bug with the DX50 you're the first user I've run across on here with that sort of problem.