So what is it about 3rd gear?

[Morety]

Are you on WoT on the upshifts? If not, that would explain it. They do shift smoothly and rapidly up but you do have to have the throttle wide open. Downshifts require a fully closed throttle and from 6th to 2nd mine shifts well but not as smoothly as using the clutch and blipping the throttle

 

[Mr Bean]

I can upshift smoothly on a positive (not wot) throttle and equally downshift on a closed throttle - all the way down to 1st. Same as on my earlier '63 plate bike.