Typically, it happens in EAC, if you mistakenly leave the "add ID3 tag" option ticked when you rip and encode in FLAC.
The ID3 tags should be removed. You can remove them by re-encoding the files using flac.exe, or you can remove them in Mp3tag in a round-about way by cutting and pasting all tags. Mp3tag won't rewrite the ID3 tag back.
See: /t/9134/1
Make sure you test this first with a very small set of files, and make sure you have backups of your test files.