OK, I think I figured this out.
It really isn't anything to do with Xpages, but with using UIWebViews within iOS.
The problem was that on the first webView, I wanted to show the iOS Navigation, but in any subsequent ones I didn't want to - would just prefer to use the web navigation.
There is a delegation method in iOS Web views that allows you to show or hide the navigation bar. I added this delegate and just check to see which page I am on. If on the first one, I show the iOS Navigation, else I suppress.
This works great!