I had the same problem and it took a while to crack it. This is a potential bug for Paul to note (I was going to put a post on the bug thread).
I found that when viewed in Mp3Tag the problem FLAC files were all marked as type: "FLAC(ID3v2.3)" compared to "FLAC(FLAC)" for files that correctly listed on the DX80. It appears that sometime last year I mistakenly had seletected the tickbox on my ripper (Exact Audio Copy in my case) that also adds ID3 tags to the resultant FLAC rip of a CD track. A search in the internet suggests that FLAC files do not need ID3, and there appeared evidence that some DAPs/music players/software seem to have some problems with such FLAC files that also incorrectly have ID3 tags added to them.
I guess the problem occurs because the DX80 reads both the FLAC tag and the additional ID3 tag appended to the FLAC file, and creates a composite tag from both.Thus getting listed files in the format "artist name;artist name", "album title;album title" and "track title;track title". Whilst FLAC files shouldn't have (and don't need) ID3 tags it appears from internet discussions on Hydrogen Audio and others that this is not an uncommon mistake, so it may be someting to consider for a later DX80 firmware, to do a check on this and ignore ID3 tags incorrectly added to FLAC files.
To solve the problem using Mp3Tag you have to select the files, cut the tag (which copies it to the clipboard), and then repaste the tag back into the selected files. The resultant FLAC files then only have the correct FLAC tagging and on a rescan are listed fine. I had to do this for about 1000 tracks which took a while, but the DX80 is now listing them all correctly. This saves the issue of needing to fully repopulate tag information as I suggest needed to be done for the similar process of converting to WAV and back to FALC again.
As an aside, the DX80 listing also highlighted a few until then unnoticed issues with my tags, such as a few tracks with space characters at the front or end, and different capitalisations (i.e. a-ah, A-ha or A-Ha).