You may lack sufficient eccentric strength to absorb and convert your horizontal momentum. Or you may have the strength but lack the muscular coordination to do so because you are not used to running at a fast speed. Or, and this is more likely to be the case, it could be that you lack a bit of both (personally, this is me, although my problem is more coordination).

Practice your running vertical with a slow jog but practice taking fast, powerful, long strides for your couple of steps just before you plant your feet for the two foot jump. The tips provided by CurtiS from axel, squatDr and AdamL are very useful. One think to bear in mind is the arm swing. You probably know this anyway but you will want to swing the arms back hard when you take your last long step / plant your first foot. Practice this and eventually, you will be able to do this faster and carry more speed into your countermovement jump.