Sorry about that, not quite sure on the precise etiquette of these forums, but I should have waited before bumping the thread. This bug is exclusively affecting the hl2 series of games, and only since wine 1.1.28. I don't know if it's a wine bug, an X11 bug or an ubuntu 8.10 bug, i really have no clue. I seem to be able to overcome it by using the show desktop command, then restoring hl2. Doesn't really overcome the core issue, but lets me keep playing, so all is well, i guess.
