The issue seems to appear when window autoHeight property is set to true. Which means that window height will be adjusted according to window contents height.But it starts misbehaving if you dynamically change the window contents – resize or add/delete new items.
Looks like the easiest solution is to call syncShadow() method on your window object.
The best place to stick it is after you modified the child controls or on window resize event.
* I haven’t tried replicating this issue in ExtJS 4.0.0 but it appeared on my 3.3.0 and prior.