I wonder if this music glitch is due to the Wii (or the GC) accessing a memory card/internal memory as opposed to the cartridge directly?
Also, I assume that the Wii version is the one with the non-Muslim offensind symbols and altered Fire Temple music - I'm only just past the Deku Tree so I don't know yet, but I'm guessing.
The N64 version I have is the one with the original music and symbols, but Ganondorf has green blood. I think it's the second batch released after the initial Gold Collector's cart, but I'm not 100% sure. I'll post up any differences I notice here.