I had a similar fault with my Suzuki RF900, the cause was rounded gear engagement dogs on the second gear set. It was OK unless you were accelerating hard, then it would momentarily jump out of and then back into 2nd, causing a hell of a lurch. I had to pull then engine out and get the gearbox repaired (new gear sets and shift forks). This happens to 2nd because there is a lot of torque involved in this shift, and also 2nd needs to be able to be shifted gently into neutral, so I believe there is less undercutting on the gear dogs. But by all means check the parts as Eric has suggested, you might get lucky and not have to split the cases.