It -could- be the tranny... if it is worn to the point that your seeing slipping, I'd expect to be seeing metallic flakes and debries in the oil. The transmission shares the same oil as the engine, so thats a good indicator of the overall health of the bike.
My tranny had a habit of leaping into neutral from second when under hard accelleration. I thought my transmission was toast, then I got the shop manual and adjusted the clutch the correct way (according to it). The problem stopped immediatly, it was dramatic.