I've observed this on iOS 4.3 to 5.0. When you create a even a simple offline web app, meaning one HTML file + few assets such as CSS and JS (all present in the cache manifest), it works offline (I tested in Airplane Mode) – BUT, when you add such an app to your home screen and open it in fullscreen mode, it first displays initial content, then everything disappears (page becomes white) for half a second or more, then content reappears again.
You can see this by adding Glyphboard, a well-known and useful offline web app, to your iOS home screen and launching it a few times. You should see the white flash effect every time you load it.
This is a big problem because it gives away the non-nativeness of an app and gives the impression that the app is non-optimized for performance and buggy.
I've tried finding reports about this but all I can find is rumors and misconceptions about the iOS 4.3 JavaScript rendering engine fiasco, which doesn't need at all be related to this issue. But in iOS version 3 I distincly remember not ever seeing the white flash.