Well, you shouldn't really expect emulation to work properly when given unconventional inputs
Safe to assume this is what you meant rather than what you typed?
Sounds about right.
Anyway, I found out that any Zelda 3 rom edited by Hyrule Magic will be considered a bad rom by zsnes. Even Parallel Worlds.
That's normal since the game's checksum isn't corrected automatically. Although, IIRC, Parallel Worlds fixed the checksum...