No idea; mine was doing that at about 6000 miles. 10000 miles later it's still fine. I asked around back then and no one seemed to know. I've actually even heard my dad's XR650L do it before.
I'd guess that it could be something to do with the piston position at firing. Maybe when you crank it over, when it's at that specific position, the ignition timing doesn't have a chance to get, well, timed and causes a nice, heavy detonation.
Maybe it's when the piston stops near the top of the compression stroke, so when you fire the engine the next time it still fires, but the piston literally isn't moving fast enough to compensate for the timing, causing the engine to knock when the piston "slowly" moves through the compression stroke.
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