Les, I understand the problem you describe and can easily replicate it.
As you have probably already determined, the problem seems to be with how CA deals with molded polylines (which I think is how they create their window casings). Anyway, you can also duplicate the issue you have by drawing a square 3D molded polyline in elevation view. Applying a brick material to the molded polyline displays similarly to the window casing in 'standard' and vector views. Because of this, I think you may be stuck with using something like a polyline slab to create the horizontal and vertical casing segments. With these you can control the direction of the 'pattern' in the material dbx edit section.
As you are probably already aware, you could convert the polyline slabs into one library symbol which would reduce the tediousness of applying it to all the windows.
Sorry I'm not much help other than to reinforce the idea that the problem seems to be how CA deals with the pattern file when applied to molded polylines.
oh, and if you haven't already submitted a defect ticket to Tech Support, this issue certainly qualifies...
Barton_Brown's post in Brick Pattern In Vector View was marked as the answer