There is definitely something odd about the audio track – I’ve seen this same behavior, but I forgot which software it was that did it (could have been a version of VLC). I’ve been using burned discs so I don’t see the problem on my hardware player. I’m wondering if the DTS lossy core isn’t the same as the DTS lossless – that way it would only appear in players that had trouble decoding the lossless. I saw the same with the audio on the official discs. To test this/fix this, you could decode the DTS-MA lossless to multiple WAVs and then re-encode it again, and then presumably the lossy core would match the lossless audio again.