Hi,
This is what I’ve been looking into. It is true that the cover art changes in FLAC seem to have helped to create this problem but the files do not need to have cover art in to fall foul of it. I read that the real problem is the size of buffer allocated in the FLAC library for handling tags and other data. I suspect (but cannot prove) that other information such as seek tables may be included in this, which is while larger files are more likely to show the problem. Some applications / FLAC libraries use a larger buffer or a different scheme for handling this data.
There is a FLAC library using version 1.2.1 in testing for Debian Etch, and I have been meaning to get around to testing it myself, but I have not yet had the spare time to play…