I use the simple sample of JSFiddle, with two windows :
<div id='jqxwindow'>
<div>Header</div>
<div>Content</div>
</div>
<div id='jqxwindow2'>
<div>Header2</div>
<div>Content2</div>
</div>
$("#jqxwindow").jqxWindow({
position: {x:0, y:0},
height: 100,
width: 300,
theme: 'energyblue',
zIndex:9998
});
$("#jqxwindow2").jqxWindow({
position: {x:20, y:20},
height: 100,
width: 300,
theme: 'energyblue',
zIndex:9999
});
This sample (and my own test) does’nt works. When selecting a window (left click), the selected becomes always topmost, even differents zIndex values.