Hi Paul and All,
Just to close the loop on this topic, my final observations in case they can be helpful for others.
In the end it does not seem to be an access problem but rather an issue with incompatible code sets. I can browse all the flawed files directly on the QNAP (via the browser interface), they look correct, they are identified as FLAC files and they can even be replayed.
Some of them look fine in Kinsky and can be played. Others do not show up in Kinsky, and in the Mac Finder they are displayed as Unix executable files. These are the files that Jaikoz will not load. Common for all of them is that they contain non-English characters from Scandinavian, German, French or Spanish language (e.g. the German operas).
This may be because some CDs were ripped with Western code set rather than Unicode, or it may have happened during the moving/uploading process. Or it may be for another reason. I really can’t tell and with OS X, Unix, Jaikoz and Kinsky in the mix many potential reasons could be investigated.
Fortunately the number of albums is manageable (maybe 50) so I have given up finding out the reasons and settled on the solution. If I have the discs I delete and reload. If not I will edit the file names via the QNAP interface to replace non-English characters. So far this has worked for all the files I have attempted to repair.