Let's think about this.
The trans design uses forks to move sliding gears to either engage or disengage, and the power is transmitted through the engaged gears.
The shift drum is what moves the forks. A spring loaded arm holds the drum in place via the star wheel or stopping plate (
http://www.cscmotorcycles.com/STOPPI...-p/z21-110.htm ) once a shift is completed. If the shift action is not fully enacted, the arm may not sit down in the detent to hold the selection, and therefore might pop up to the top of the ramp of the stopping plate, giving a false neutral. A bit more vibration and the drum moves to select the next lower gear.
If the fastener that holds the stopping plate is loose, that can cause the "short shift" action you are experiencing. A worn/defective pin in the 5-6 gear selector position can do the same thing.
There are other possibilities, including bad bushing, gear, shift fork, etc.
If it were happening to me, I would remove the right crankcase cover to be able to inspect and watch the action of the shift linkage.
Good luck.