So whats the deal with fork length?

Why is it that so many dirt jumpers and 4crossers run relatively low front ends (80-100mm). When I set my bike up that way it feels really akward. I used to run a Spesh P3 and had to swap the 100mm with 125mm forks and even stacked the stem a little higher than normal and only then it felt right to  me.

I am picking up my new SX frame today and I need to think about stack hight so I would appreciate some wisdom and experiences.