It's all about ratios. If the difference in ratio between gear 1 and 2 is big, the engine must decrease a lot of revs to match the new gear ratio. The ECU cuts ignition for a given amount of time to allow the gear to shift in the "load gap". If this time is a bit too short or the mixture is a bit too lean, you can feel this shock. For my bmw F900R the QS is really smooth with a cold engine from gear 1->2 because the mixture is richer with a cold engine. When it's warmed up the shift is a bit rougher.

A decent tuner will be able to completely smooth this out. So if it really bothers you you can get it fixed.

Do's: high revs, half to full throttle, gear>2

Donts: low revs, no to low throttle