I'm not sure where to put this bug report, but I'll try here.
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I have an IPS and a UPS that both change a ROM image in the EXACT same way. I tested with a hex editor. However, only the IPS, when placed in the appropriate folder, will cause any change in the game when soft-patched.
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In this case, it is a English translation patch for Fire Emblem - Fuuin no Tsurugi. The UPS, despite causing the same effect as the IPS when hard-patched, just doesn't seem to be read by VBA-M's soft-patching ability at all. This is strange, because it can read the Mother 3 English translation patch just fine.
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And yes, the files are all named correctly.
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I have the newest VBA-M (SVN891), but this problem occurred in every version I've ever used.
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I took some pictures, though I think they may be useless for this bug. I copied the images from my monitor because, for some reason, VBA-M is crashing when I try to screen capture. The differences in color around the "Press start" is because the green aura flashes as a part of the normal game.