You should probably change your resolution. You can access the game configuration by clicking on configtool.exe in your game directory. 1024/768 is a good choice if your system supports it.
You usually get the chance to configure the first time you play or if you bomb out in the game. When you first install, the game defaults to a good configuration for your computer, but if you bomb out and don't reset it manually, it picks a low one. I had problems with that - having windows overlaying characters, etc.
