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This is not a problem that I’ve heard of before, therefore I’m not going to be much help in diagnosing it. It kind of sounds like that’s just the way it is.
You modify the bike, it changes the way it feels, you’ve gone over the work, everything looks great, someone double checked the tune, the bike runs brilliantly otherwise……the only thing I can offer is “that’s the way she goes”. I’d be happy to take a look at it in person and give it a real diagnosis…