no really sure of your problem. the only thing I can think of is running at high speeds and locking the rear brakes up it will make the rear hop a little causing some vibrating on the rear supension. you may want to check the swing arm to make sure it doesn't have and slack. check all the bolts on the rear end and/or a loose axle.
I have the same problem with my rubi. Dealer said its the trans downshifting, but they had no explanation of why it would happen when in manual shift mode. At that point they told me it has something to do with the way the engine brake works. So I don't know, sounds like they were just blowing smoke up my arse.
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