Let me complete my own answer with demo material for the readers:
Voya-Ger music comes from the intro of Sentinel 2 diskmag:
http://janeway.exotica.org.uk/release.php?id=7153
Ramon music comes from Music Invasion 3:
http://janeway.exotica.org.uk/release.php?id=1885
El Loco & Marlin music from It's Just The Beginning musicdisk by Paragon:
http://janeway.exotica.org.uk/release.php?id=8177
Quick music comes from 2D Demo III by Oxygen:
http://janeway.exotica.org.uk/release.php?id=10038
Now, it happens, but it's really rare when a "rip protection" is set up. Generally, an unsupported effect is used for syncing matters.
However, there are only two of them in the whole music ...
The next step, as far as I am concerned, would be to contact the author. I won't touch the music on the simple ground that "it doesn't sound right".
In a general way, I believe there are many many more "broken" (i.e. don't play correctly or are downright corrupted) musics out there. Still, there's no small victory
So please report those so that we can investigate.
btw, did you liaise with Saga about Modarchive ?