And you don't have any cover art anywhere else?
I suspect the problem lies in how art is stored in the flac files (without a name). When MC goes to retrieve it (which I suspect it does several files at a time), whichever one gets there first wins, and several end up with the same image. In this case, it probably is the plugin which causes the problem.
Cover art is pretty new to flac, and so the plugin just extracts to a simple "cover.jpg" filename. I'll probably have to implement some checking and number incrementation to make sure they truly are unique.
You might be able to verify this by doing single albums at a time and see if works correctly that way. If it still fails, then I'm not sure what the solution is.
I don't have any jpg/png/etc graphics files in the directories in question, all images are stored within the flac files.
I agree with your idea about creating a check/incrementation to make sure the file names are unique. An alternative might include create a "cover-[chechsum].jpg" or "cover-[crc-32].jpg" files based on the flac file name itself, or even use an MD5 checksum (which might be too long). Just a thought.....
Now regarding your suggested test:
1) Importing of a folder (9 songs) results in two songs have no thumbnail art (flac_cover.jpg might have disappeared).
2) Dragging and dropping one file at a time into the library resulted in perfect thumbnails
Now, in order to perform the above test I had to completely delete the existing library and restart MC. That particular situation does sound like the problem aussie1 suggested but I'm more concerned with the above problem and your suggested fix.
Thanks!