99% sure that the engagement dogs on the gears are buggered. I have a big box of gears with buggered dogs if you want them!
Other issues that cause this are bent shifter forks, which even if straight now will get bent if you continue to use it.
I did three gearboxes in the '96 season (SP rules), whereas in '95 (SS rules) I used an F3 box and has absolutely no problems whatsoever. It cost me a place at Shah Alam on the run to the finish line as it started jumping and I got beaten by a wheel.......Damn those cheesy gears!
If you have the enthusiasm you need to pull out the gearbox and take a look at the dogs. You'll probably see rounding of the edges, and if so they need changing. You don't need to drop the engine to pull out the transmission cassette and it's quite straight forward.
Changing the gear selector cog and spring to that from an MC21 gives more positive engagement, and if you round off the corners of the neutral part of the cog then it'll never go into neutral by accident between first and second......then again, it'll be frustrating to get it into neutral at all! But hey, if it's a track bike then just kill the engine.