Odd. Is it only this file set that is affected? Are the files protected by some permission rights, locked in any way? If you can't check/change file permissions -

You could try:

1) creating a ffp file of the original flac set.
2) decode the flac set to wavs in another folder
3) encode the resulting wavs to a new flac set.
4) check ffp file against the new file set, if identical, try creating your torrent file.