Mercator seems to have it right on, although I experienced something a little different. My page elements all have 3d transforms and when my Disqus dialog box popped up to sign in before posting a comment... the mouse was not interacting with that layer (even though it was being rendered above the 3d transformed layers). What was interesting is that the dialog box with a fixed position was not a descendent of the containers with the 3d transforms.
I had this markup:
<body>
<div class="book">
<div class="page">
<div class="front-side">stuff</div>
<div class="back-side">other stuff</div>
</div>
</div>
<div id="disqus-dialog">dialog stuff</div>
With the .book container with a perspective and 3d tranforms on the .page, .front-side, .back-side elements. (I'm using dice.js to load my CSS from json)
'.front-side' : {transitionAll:'400ms', padding_bottom:'150px', position:'absolute', width:'100%', _webkit_backface_visibility: 'hidden', _webkit_transform: 'translate3D(0,0,1px) rotateY(360deg)'},
'.back-side' : {transitionAll:'400ms', padding_bottom:'150px', opacity:'0', position:'absolute', _webkit_transform: 'translate3D(0,0,-1px) rotateY(180deg)', width:'100%', _webkit_backface_visibility: 'hidden'},
But notice I have the translate3D(0,0,1px) and translate3D(0,0,-1px) and I was unable to interact with my fixed position dialog.
I changed the translate3D styling to this :
'translate3D(0,0,-1px) rotateY(360deg)'
'translate3D(0,0,-2px) rotateY(180deg)'
...and voila! My dialog was now responding to mouse events, but of course now I can't interact with the 3d transformed elements.... what gives?
Strange business, but way worth the effort to fix this. 3d Transforms rock socks... my working site can be seen here with the disqus plugin -> highdensitygames.com