Joseph Wisniewski , May 16, 2011; 05:18 p.m.
Yes. It would affect the stacking greatly in CS5. The change in perspective with each change in focus produces strange looking boarders on edges of objects. This is called by several names, like "fringing" or "ringing". CS5 does not handle it well, some other stackers, like CombineZ, Helicon Focus, or Zerene Stacker, do a lot better.
The longer the lens you use on the rail, the less fringing you'll get. If you have a 200mm, you'll end up with a 10:1 subject-size to perspective point distance, and minimal fringing. An "infinite perspective" lens totally eliminates fringing, but telecentric macro lenses are insanely expensive. There's a technique for coupling two lenses with a telecentric stop between them that's surprisingly cheap and easy.
Or switch to a bellows, and use "bellows draw" (rear standard movement) for your focus stack. That gives you a finite (and very short, if you want) perspective, which might look more natural for many subjects than the "infinite" perspective and total "flattening" you get from the use of long lenses or telecentric photography.