You might want to practice more or get your car checked out at the dealership. I've heard about people having trouble with the 1 - 2 shift with the 6 MT.
When I first got the car it took a few days to get a smooth 1 - 2 shift, but it had nothing to do with the throw between gears. It is a little jerky getting used to the higher engagement point of the clutch.
Now, shifting is fast and smooth between all gears.
If you have a difficult time actually getting the shifter from 1st into 2nd gear, there might be something wrong with shifter/transmission. If the shift is jerky, it will just take some practice.
E92 M3 | Jet Black | All OEM Everything
E30 M3 | Alpine White | Mostly OEM