To everyone having issues with Frue Lufia or the other hacks, learn from my pain.
Most ROMs these days (that I'm certain we're all acquiring legally) are unheadered, and have a ROM signature that looks like this:
Lufia II - Rise of the Sinistrals (U).smc
Size: 2,621,440
CRC-32: 20F2AC29
MD-5: 6efc477d6203ed2b3b9133c1cd9e9c5d
You need some program to add a header; I used Tush, which you can get here easily enough. After adding a header, your ROM should have the correct information:
Lufia II - Rise of the Sinistrals (U).smc
Size: 2,621,952
CRC-32: 2FAEBB78
MD-5: d35fcf90c273d4bc12eed59120954e58
Here's the part that I think is screwing everyone up: I was *trying* to get this to work with Snes9x's Retroarch core. It ran the "normal" Lufia II fine, but would not run Frue Lufia, even when the patch was applied to the correct ROM. I think this is what was causing everyone to *assume* the patch is at fault. Nope, it was Snes9x. After spending two hours fighting this, I upgraded to the latest core, and shockingly, it now works. So I think the real problem most users have been running into has really been an emulator issue, not the patch itself.
No idea why the patch necessarily caused issues when the base game ran fine though...

Hope this helps; wish someone figured this out about two hours ago.