Collision detection with .mdl occurs in two different ways.
Models collide with level geometry based on the level hulls and the 'orgin' of the model.
Models collide with other models based on the 'bounding box' of the model.
If your model is moveing through level blocks then check where the orgin of the model is. I have made the mistake before of haveing the orgin at the very base of my model. I could then walk through walls i.e. a human model with the orgin at the feet instead of the mid section.
If your model is moveing through other models then you may want to adjust the MIN_X, MIN_Y, and MIN_Z values for the model. These will essentially adjust the size of the bounding box for the model.