Id3 tags are busting your flac party (especially with acxi/oggenc choking with ERROR: Input file [...] is not a supported format)? Just grab yourself a copy of id3v2 and run it like

id3v2 -D ./*.flac

If you're rocking the party with Arch Linux, you can find both id3v2 and acxi in the AUR.

There, that fixed it.