Is it only the ID3 byte sequence, or does it really create ID3v2 tags? If it does generate ID3v2 in FLAC, check your configuration? I’m pretty sure dbPowerAMP uses “OGG” style tags for FLAC by default. If you can’t stop it from writing ID3, it’s time to report it to Spoon (the author). Bug.
ID3 tagging is not recommended for FLAC, though it is valid in a sense. If Firefly does choke on it, I guess it’s a bug, too. But it’s best to avoid it…