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See, this IS the problem for me. Since the 1986 - Pokemon Emerald (U)(Trashman).gba file isn't the right source file, the patch will not be applied unless I select the ignore option in NUPS.
However, when I do that, the file is not patched correctly. When I open it in VBA, the rom runs, but...
So I hate to just sound like so many others, but I TOO am not able to find any ROM that this game is compatible with. If anyone could pm me a link to either the correct Emerald ROM or a valid earlier build that would be AMAZING.