I've got no answer to the bouncing clock problem, but too large windows imply that you've chosen too small screen resolution. Change the screen resolution bigger and you get smaller windows. You should be able to do this by opening a terminal window, then using the "su" command to become SuperUser, and then typing "dpkg-reconfigure xserver-xfree86".
The version of Debian that you now have is pretty old, not ideal for desktop use. You might get a better system (possibly without bouncing clocks) if you try the new Sarge installer that gives you a newer version of Debian: