Rob I know that some Fastrack switches come with tiny "make-up" sections that can optionally be omitted when making a crossover between parallel mainlines. Did you buy your track brand-new? Is it possible that you've included the makeup sections in some cases, and not in others? Or perhaps accidentally omitted them?
How about posting a photo? I can try to recreate your layout in other layout design software such as SCARM and RR-Track. I think you can download a limited demo version of SCARM for free. However, to get to the root of your post, I find it hard to believe that Lionel would make switches with a different geometry than the curves they are intended to replace. As an occasional creator of Fastrack Christmas layouts myself, I'm following this thread!