Testing with iOS Simulator - iPad - 7.0.3 Titanium SDK: 3.2.0 NavigationWindows do not respect zIndex settings and instead are stacked in the order in which they are opened. Changing the zIndex after the NavigationWindows are opened has no effect. When these 2 NavigationWindows open you *should* see the green NavigationWindow (top) taking up the…

index.js

$.top.open();
$.bottom.open();

// If we open in this order it works properly
//$.bottom.open();
//$.top.open();

index.xml

<Alloy>
	<NavigationWindow id="bottom" zIndex="0" top="0" height="75%" backgroundColor="#ff0000">
		<Window></Window>
	</NavigationWindow>

	<NavigationWindow id="top" zIndex="9999" top="200" height="Titanium.UI.FILL" backgroundColor="#00ff00">
		<Window></Window>
	</NavigationWindow>
</Alloy>

Confirmed in 3.2.0.GA. Same behavior in classic:

var windowBottom = Ti.UI.createWindow();
var windowTop = Ti.UI.createWindow();

var bottom = Ti.UI.iOS.createNavigationWindow({
zIndex:0, top:0, height:"75%", backgroundColor:"#ff0000",
window: windowBottom
})

var top = Ti.UI.iOS.createNavigationWindow({
zIndex:1, top:200, height:Titanium.UI.FILL, backgroundColor:"#00ff00",
window: windowTop
})

top.open();
bottom.open();