Okay, thanks. More details for you. I found that changing the theme does make a difference. Some themes are fine, others not. Here is the test I used:
I wish I had captured this with a better theme, but it still makes the point. You'll see three windows. The upper one (with focus) runs the horizontal length of the picture. The one below it on the right extends a little over 45 pixels. The one below on the right extends much further. You'll see two scrollbar arrows and be low that a horizontal line above the work "IN." That line is about 60 pixels below the edge of the upper window with focus.)
In a normal scenario, you can give the focus to either lower window by clicking 1 pixel below the top window's edge. This immediately activates that window and it jumps to the top level, covering the other windows.
I don't have many themes loaded, but I found this default (correct) behavior when using these themes:
Mac OSX Ultimate
The following themes cannot activate the lower left window unless the click is about where the vertical line over the "IN" is near the 60 pixel mark. They cannot activate the lower right window at all. The upper window must be moved up at least 15 pixels to expose more of the lower right window before it can be selected:
Lastly, I found a few themes that fell in-between. With these themes loaded it is possible to activate the lower right window, but only by clicking near the very bottom of it:
With themes that work correctly, hovering the mouse over one of the lower windows results in the cursor changing to the appropriate shapes, so it is reacting to the unfocused window below. For instance, moving the mouse even 1 pixel below the active window results in a horizontal-double-arrow if the cursor is over the vertical border of a lower window or a vertical-double-arrow over a horizontal border. But when the problematic themes are loaded, the cursor doesn't change until it is moved all the way down to the horizontal line at the 60 pixel mark.