DVD vs Theatrical version?

Anybody have any idea why the DVD version is so different from the theatrical version? I absolutely loved the film when I saw it in theaters (twice). The cut scenes flowed nicely and it was a fantastic narrative. When putting the film to DVD however, the editing and order of the film was completely changed (confusing/boring). It is a real shame that the Darwin's Nightmare wasn't simply transferred as it was to the DVD format.