HD Tracks missing bits in flac and metadata(?) probs.

I use HD Tracks download manager and have found that, since the ndac can accept flac and I no longer have to convert to wav, the start of some songs is softened as though it loses the initial transient pluck of guitar or similar. I normally put Hi-Def straight to USB stick in the native format.

So, I thought a little experiment would be in order and converted one of my "problem" HDT albums (Paper Airplane) to wav using MAX which I've set up to import into iTunes on my MacBook at the rate downloaded, these are then played back via Pure Music and HiFace into the ndac. Eureka! The start of things returns. I have not yet put the wav versions to USB to try that way but imagine this will work fine.

Has anyone else found this problem? All my flac albums from Naim and Linn work perfectly without faffing around. So I'm happy to have sorted the issue but would like to know why it happens.

Also, some albums from HDT play in the wrong order, even though they're numbered correctly and appear in order on the listing. Is this a metadata problem and how can I solve it. The HDT album folders do not seem to contain a file for metadata (and I don't have a clue how to fix it anyway)?

I'd be grateful for any help