Is it possible that the little O ring that fits in the cover where the bottom bolt goes through fell out? I'm not sure if it being missing would cause your problem, but Yamaha must have fited it for a reason.
You should be able to remove the cover to check for this without draining the oil if you put a block of wood, or similar under the back wheel so that the bike leans more than usual when on its side stand (but a little will leak out)
Good luck
Mark
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