IMHO: It's rider abuse. Get up to 80, 90 mph, start coasting, then around 60, pull in the clutch and because there's a red light in the distance, start downshifting 6-5--4-3-2-N. By the time it gets to 2nd you might be down to 50 mph (just rolling along) -- that's too much backlash on the gears because the engine is at idle, even if the clutch never engages. Slamming 1st-2nd under high throttle with no clutch also tends to help it along. As does shifting really slowly (or incompletely) 1-N-2, letting the gears dance off each other (a common newbie mistake for people used to shifting cars gently because of the planetary gears).

Cheers,
=-= The CyberPoet

As I recall reading about this problem, its also because the change in gearing from 1st to 2nd is numerically greater than a gear change from 2nd to 3rd, 3rd to 4th, etc. So 2nd gear gets the most shock of all the gears. Ist gear shock from a standing start is absorbed a lot by the clutch. And people just don't have that many opportunities to really hammer it into 5th or 6th. You'd be doing way over 120 mph. All from my recollection only.

As for backlash? So the gears are meant to absorb greater shock from acceleration, but not from deceleration I guess.

I do notice a harder shift into 2nd than other gears - the clunk is a little louder too... :\

I agree from first to second if the rpm's are not just right it will clunk

also make sure your bike warmed up properly before you go out. Making sure the oil is flowing throughout the engine will help in the longevity of your bike. If the bike is cold then it will be a little more clunkish.

No, they're cut in a way that doesn't make any difference in that sense -- the problem is RPM level at the engine vs. speed at the front sprocket (the differences have to be taken up somewhere -- usually the rear sprocket cush, then the chain & sprockets, then the tranny). Going up the gears, you're unlikely to be all that far off in RPM levels compared to what would be an ideal mating speed...
Example 1: engine at 6k rpm, switch 2nd to 3rd without changing RPM's, you're still only about 1200 RPM off of where it should be for an ideal mating. Ditto on a fast downshift with gear engagement at each gear.
Example 2: But if you're doing 6k in 6th and you start clicking down all the way to neutral quickly without waiting for the speed to drop (without using any engine braking nor disengaging the clutch at each gear), by the time you get to 2nd gear the ideal matching speed would be around or beyond the redline of the bike -- with the RPM's having dropped to idle by now. And that difference in gear speeds has to go somewhere. The speed difference in our last case is what I think tends to eat up the teeth and bend or break the outer edges of the gear faces as it tries to mate (mechanically, the two common reasons 2nd is bad are bad teeth and/or bent shift-forks; bent shift forks come from forcing it together under strain normally).

Cheers,
=-= The CyberPoet