Interesting, I think the box is one of the best features of this car. It has a solid feel with no free play and a short throw.
I've had no issues with mine at all, I guess you just have to be smooth and steady with it, resisting the urge to change too quickly.
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Fair comment, when my box changes smoothly from 1st to 2nd, it's great and I agree the short throw and feel of the box is really nice, it's just that frequent clunk as it goes in.
I've only owned my car from few months, it'll be interesting to see if it gets better in the warmer weather!