Are you running with compiz turned on or off? I have to wonder if you change it, would it make any difference? Go to System -> Preferences -> Appearance -> Visual Effects. If it's set to Normal or Extra, try setting it to none and then launching your game. It may or may not make any difference but it's worth a shot. I am running Ubuntu 8.10 with wine 1.1.20 and I don't have that problem with any HL2 based games. I did have this problem at one point when I installed DirectX 9.0c and was trying to launch the games using DX9. If you have the official DX9 from Microsoft installed, I would suggest you get rid of it. It seemed to cause me nothing but trouble. :/
