Bumping this thread since an answer is still wanted.
I think this might be happening because you have not put a new offset with free space into the box that says "Base destination offset". The offset that is normally in that box is apparently the one used for the original song's notes, etc., and if the song you are inserting is bigger than the original one it will end up eating into the next song and corrupting it. You have to use an offset that has enough FF bytes to hold the whole .S file.
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