Hi Scottte,
The window.scrollTo(0,0) trick does work - as long as the screen does not scroll, when I'm not wrong.
An additional possibility is to add the following meta code to the header section of the iPhone template, so when creating an application shortcut to the Web-page and launch the Web application using the shortcut, the iPhone Safari shows your Web-App in full screen - works since iPhone OS 2.1:
<meta name="apple-mobile-web-app-capable" content="yes" />
Would be perfect, if these "features" will become standard (or configurable) in MobileJoomla.
Reference:
Apple-Specific Meta Tag Keys
-Kurt.