2 reasons, trying to put in gear to soon after pulling in clutch, and I use 20 w 50 Amsoil in all three holes . I did a service on my buddies 09 ultra using Amsoil and
he could not believe how better his bike shifted and it was also cooler & quitter, I also see people really slam the heel shifter . Just my .02 worth
They don't after you get tuned into them - except that first gear after a long stop. That is due to the clutch plates sticking to each other and cold oil.
They only clunk if you bang them into gear too quickly after pulling in the clutch, or if (like on MOST bikes)the clutch is improperly adjusted.
It's called "gear clash" and it's not good for the gear box.
I switched to Formula+ in the primary and Amsoil SevereGear 75w110 in the trans, still get a little clunk going to 1st, but mucho quieter,
and not at all while shifting on the move.