bj wrote:Started to take it apart, and noticed that the nut on the leaking bolt has a groved bottom. Could that have cause the problem?

Well, it's not helping that's for sure, Honda used smooth bottomed nuts for a reason and no matter how you "torque" it up (wheather it's with a torque wrench or the more usual torque wrist) it'll end up different to the rest, add to that once they've leaked gaskets don't like sealing.
It's not like it's the world biggest job anyway so just change it, use a proper nut and double check the cylinder and crankcase faces are clean.
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