I figured out one of the wonders of the world, and its name is F11. I took the following picture once I come up with a theory:
It turns out the bounding box is incorrectly set, and as you can see the box is indeed set on the ground, it just so happens the model that is supposed to be in the box isn't necessarily in it. For those who are curious, the number in the top right corner is c_trace telling me how far the model is to the ground, so it seems I no longer need any help.
EDIT: I've found the command to update the hull of the entity, input something similar to
Code:
c_updatehull(entity, frame);
to update an entity according to the frame. The problem is fixed, hope this helps anyone with similar problems.