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@beardalaxy IIRC, the N64 stuff was from iQue's servers while the SNES, GB, and GBC were from NOA's servers. (I guess they were dumb enough to use the same password)
There is also a bit of evidence that the DX version was actually made by reverse engineering the original B&W version instead of using the source code.
https://www.pagetable.com/?p=28
Either way, I find them putting the original B&W ROM without patching it incredibly lazy. That version was notorious for game breaking bugs. It was probably the reason why the DX version was on the 3DS Virtual Console instead of the original version.
@beardalaxy Okay. New theory: Nintendo of Japan only kept the source code until they were completely done with whatever game they were working on. They send the source code to NoA, NoE, iQue, etc for localization. At least NoA and iQue preserve the source codes to those games, while NoJ deletes the source code when they are done with it.