Welcome to the forum arstrock.
Knifemaker may have this nailed, but I'm a little unclear on your exact issue. I've never heard of this before.
Is the bike new to you?
Did this just start happening?
Are you an agressive shifter?
Does it happen every time you are "revving" through second, or just sometimes?
So, in second gear, when you are rapidly accelerating, the jerking starts and continues until pulling the clutch for third gear?
If you let off and then throttle again, does it stop?
Does it still jerk under more normal acceleration?
Have you gone through adjustments to the cable, clutch lever?
Have you changed the oil lately? What are you using?
Where do you live (climate)?