I have the game on steam, just installed it again, and the same problem is around. I run the game, pick window mode, logout. The game starts, usually in window mode, and I can play fine. Although if I load a mod the game goes back to fullscreen. And the next time I run the game, 50% of the times, it also goes back to fullscreen and I have to turn on window mode and re enter the game. Its soooo annoying. Anyway around this? Write copy protection on some file or anything ?