I've replaced my video card and am now having MUCH better results with CounterStrike:Source (I love Wine!). Most of my problems were due to a defective EVGA 9600GT.
However, I discovered a new windowing bug today with CS:S and other Source-based games (I verified the same behavior under the Zombie Panic total conversion) running under KDE4.1 (no Compiz, Kubuntu 8.10b1).
Do this:
1) Start CS:S on your first desktop. 2) Configure CS:S to run in windowed mode in a window smaller than your desktop. You should see a CS:S window with your standard KDE windows decorations. So far, so good.... 2) Use the pager applet to flip to a second desktop 3) Flip back to the first desktop. 4) At this point you will see not only a window with your standard KDE windows decorations, but inside that window will be a Windows window with Windows decorations. All mouse clicks will be offset by the number of pixels equal to the second, Windows, titlebar. (You have to click below everything)
You can recover by using the Windows titlebar to maximize the game window - which will maximize the KDE window and get rid of the Windows window. Then, flip to the second desktop. Flip back to the first desktop and you will again have a Windows window inside your KDE window again. Hit the restore button on the Windows window, and the KDE window will shrink back to normal size and the Windows window will have disappeared. Wow, that's some redundant use of the word "window".
I hope some dev can make sense of my rambling and use it to improve Wine. Thanks.