My 500 did the same thing for a bit when I first put it on the road. I'm not certain exactly what was the problem as I made a lot of changes in the gearbox when I fixed it. My suspicion is that the shift cam plate is worn. I would disassemble the gearbox (requires tearing down the primary too) and inspect everything. While you're there, do the plunger spring, bearings and seals, and rebuild the clutch ramp / shift mechanisms. (springs, balls, etc) Either do NOT disassemble the shift 'fingers' or plan to fabricate pins to hold them in as modern cotter pins will NOT hold them and they WILL fail and you'll be stuck in (or between) gear. (I rode mine home with 2nd, a false neutral and 3rd when mine failed ... I had to drill the outer cover to get back into it)
My guess would be that between the camplate and the plunger spring, you'll get it ironed out.
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