I am using Ubuntu 10.10 on an Intel Core i5 with an NVIDIA GeForce GT 330M using the NVIDIA binary drivers version: 260.19.06.

Steps to recreate:
Run Blender current official beta 2.56.0 r34074.
Scale the window down and up vertically and horizontally by grabbing the lower right corner.
Eventually, the scaling function will get caught up and will continually cycle the vertical scaling of the visible interface elements no matter which direction you move the mouse creating a black box at the bottom of the window that is dead space.

It appears that the panels don't have a minimum size setting, and are literally getting scaled down to zero and disappearing into oblivion. I'm not sure what might be causing the large black area to appear. It is almost as if the bottom of the view port becomes detached from the bottom of the window and doesn't know how to find its way back.

I downloaded 2.49b and a very similar problem occurred. I captured the output when I ran 2.49b, and it gave me the warning:
"Warning, removed zero sized window from screen 3-Material"
2.56a does not report such a warning.

I have also tried running Blender 2.56a Win32 through Wine, and I can achieve the same effect.

I asked on BlenderArtists and on the blendercoders IRC channel and no one would try to recreate it on their system. Therefore, I was only able to test it on one computer.

Here's a link to a Youtube video that displays the behavior:
http://www.youtube.com/watch?v=vbi4QYKxSAM

I'm also uploading an image that shows what the black box looks like. it happens with the default .blend file on both 2.56a and 2.49b, so I won't be uploading a .blend.