Our web app requires a fixed header. We are fortunate in that we only have to support the latest browsers, but Safari's behavior in this area caused us a real problem.
The best fix, as others have pointed out, is to write our own scrolling code. However, we can't justify that effort to fix a problem that occurs only on iOS. It makes more sense to hope that Apple may fix this problem, especially since, as QuirksMode suggests, Apple now stands alone in their interpretation of "position:fixed".
http://www.quirksmode.org/blog/archives/2013/12/position_fixed_1.html
What worked for us is to toggle between "position:fixed" and "position:absolute" depending on whether the user has zoomed. This replaces our "floating" header with predictable behavior, which is important for usability. When zoomed, the behavior is not what we want, but the user can easily work around this by reversing the zoom.
// On iOS, "position: fixed;" is not supported when zoomed, so toggle "position: absolute;".
header = document.createElement( "HEADER" );
document.body.appendChild( header );
if( navigator.userAgent.match( /iPad/i ) || navigator.userAgent.match( /iPhone/i )) {
addEventListener( document.body, function( event ) {
var zoomLevel = (( Math.abs( window.orientation ) === 90 ) ? screen.height : screen.width ) / window.innerWidth;
header.style.position = ( zoomLevel > 1 ) ? "absolute" : "fixed";
});
}