Is the reference part at some distance from the rest of the parts in the view? Reference parts are not taken into account when calculating the extents of the view, so the view is essentially cropped around the "real" parts. You can adjust this view margin in the Edit View box, Model State tab. The margin shown is what Inventor calculated, but you can increase it in order to pick up reference parts that may be partially or totally left out of the view.
Don't know if that's what's happening in your case, though, since you haven't posted any images or files.
