if it IS a header issue, i'll try e-mailing the author so he updates his readme because there were no mentions of whether or not headers would screw anything up.
I'll give you it should always be mentioned in the readme for good practice, but I don't think you understand what the header is and how it influences the patching process.
Having a header or not having a header changes the SIZE of the ROM file. An IPS patch is simply a collection of instructions like 'At offset XXX change this byte to YY' or 'At offset XXX stick twenty-three 00's'
SO.. if you don't have a header and the patch was based on an original ROM that did, ALL of the offsets are WRONG and it could cause a variety of problems in the game. The same can be said if the patch was based on an original ROM that did NOT have a header and yours does. Again, all the offsets will be wrong and it can't be patched correctly.
It only patches correctly when the ROM you're using is the same size as the same one he was using.
For clarity, I should mention that the actual information contained in the header doesn't matter (except in a rare case the header was modified, but there should be no good reason for this in SNES translation patches). All that matters is if there IS or is NOT a header.
In summary, there's usually only two possibilities when it comes to SNES ROMs. If you have a valid clean ROM, try patching with a header and without a header. One of them should work. If neither do, you may have other problems such as dealing with an interleaved ROM or patch based on interleaved ROM, or corrupt/different ROM than the one the patch was based on.
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