This thread here shows the latest status of Mp3tag concerning this situation:
Strip ID3 tags, leave Vorbis tags on FLAC?
His answer expresses the official status.
But it is true some programs do add ID3 tags to flac files( - in fact any file type could have an ID3 tag). But we'd like to stick to the official guidelines
You should also check your EAC settings [F11] and disable Add ID3 tag or any other optoins that add ID3 tags.