I had exactly the same problem on my first engine and gearbox. I changed the 3 dog legs selectors and shafts they were on, was ok for about 400 miles. In the end I found another engine/gearbox and threw that in.
then it started to do the same thing again, I tried to live with it, untill I pulled away from a set of lights in first, went for 2nd gear and she jammed in neutral half way round a round about!! so welcome engine number 3!!
Later I was told I should have changed the dogs/selectors, shafts and selector drum
Ive owned my FZS600 Fazer for 10 or 11 years and will never part