the window sill is set higher than the cut plan of your view range - or the window head is set lower than your view range, it will not cut the way you want it to. If this is the case, use the 'Plan Region' (View Tab, Plan Views pulldown Plan Region). This will allow you to create an instance in the location you choose to change the view settings.
Create a rectangle around the window that is not cutting appropriately with the Plan Region tool and then set the view settings of that particular plan vregion. I find this helpful in basements where the windows are close to the ceiling, sometimes around stairs where I want the cut line in a different place and even fireplaces where the opening to the fireplace is below the cut plane.
Let me know if this works for you.