Version:            (using KDE 4.4.2)
Compiler:          gcc 4.4.3 
OS:                Linux
Installed from:    Ubuntu Packages

Steps to reproduce:
1. Open application A (must support multiple windows).
2. Open a second window in application A.
3. Open application B.
4. Make one of the application A windows be on top.  If you were to press the window-switching shortcut now, application B would be on top.  That is, the lowest window is one of application A's window, the middle window is application B's window, and the top window is application A's other window.
5. Close the top window.
6. Now, the one window from application B is on top, but the other window from application A has keyboard focus!  This is bad!

Here's a scenario where this is problematic.  I have two Firefox windows.  In between them in the window order is k3b.  I've been browsing for a while in the Firefox window that is on top, and I have forgotten about k3b.  I close the top Firefox window.  I see the k3b window and press Crtl-Q to close it.  Firefox closes instead.  FAIL.

In general, any window that is automatically made topmost should also be given keyboard focus.