Jeff, you hardcoded many links in the javascript file, which might be the root of the problem. I just had a very quick look at the files anyway

example:
document.checkout_payment.action = "index.php?main_page=checkout&action=process"

You should use zen_href_link function here.

On another hand, if you use SSU, you can exclude these pages from using SEO links in admin. For example, just put "checkout" without the quotes into exclude list in ssu admin settings.