Not sure if this is a real issue or not, but a bit strange.
If you have firebug open, some (but not all) windows try and open in the center of the full-sized window (i.e as if firebug wasn't there), or at least that's what it looks like could be going on.
This seems to cause the layout of the page below the window to change it's size, which is the odd bit.
As I say, some windows appear in the middle of the visible area, whilst other try and go in the middle of the full browser window, but hit the bottom of the viewable area, pushing the rest of the content up by the offset.
Appreciate that's a little hard to fathom, so have attached some screenies illustrating the point.
PS: Oh, should mention they both use the same window class, which does nothing other than set a few common config options.