Interesting, that did fix it. It verifies fine now! Awesome thanks for the suggestion!
So my log on this Omega Ruby:
1) Wouldn't boot.
2) Ran verify, failed.
3) Ran fixer, 150-ish unfixable errors
4) Game booted (I was curious).
5) Ran fixer, 0 errors.
6) Ran verify, failed.
7) Ran fixer, 0...