I had this problem. I tried a number of things, none of which worked:
- Changed the oil
- Adjusted the clutch cable
- Raised and lowered the shifter
- And probably some other adjustments that I don't remember.
I had another problem, which I thought was unrelated: a loose right-hand control housing assembly. That's the black plastic item on the right handlebar that the start button is on. To call the assembly "loose" is overstating things. There was some freeplay, a few millimeters, whenever I twisted it back and forth.
More to the point, the freeplay in the control housing assembly meant that the throttle tube had freeplay, too. So the throttle had freeplay that it shouldn't have had. (The throttle tube is supposed to have a couple of millimeters of freeplay, which you adjust by loosening and tightening the throttle cables; the problem that I'm describing is separate, and in addition to, that.)
So I replaced the control housing assembly, part 46091-0217, which I bought from Ron Ayers. And after I replaced it, I no longer had a problem shifting from second to third under hard acceleration.
The control housing assembly had become loose when I manhandled a new grip onto the throttle tube, with a grip warmer between the throttle tube and grip. There's a round plastic tab sticking out of the control housing assembly that fits into a hole in the handlebar. When I manhandled the grip onto the throttle tube, that round plastic tab got deformed, thus allowing freeplay.