I would suggest you use Byuu's excellent emulator to test the roms before burning them to the flash chip. BSNES will only load files if they're headerless, de-interleaved and proper (exactly what they were as data inside of Nintendo's ROM chip.
And there's a tool which comes with BSNES that does "purify" the roms for you, cutting headers, identifying and renaming them to ".sfc"...
Great stuff that makes life easier.
