I normally have my taskbar at the top of the screen. When I launch 2000:1:A Space Felony, it continues to show my taskbar. If I set the taskbar to auto-hide, it just shows a strip of my background wallpaper where the taskbar would normally be when open. I had to move my taskbar to the bottom of the screen to get the game to display correctly.
I wish there was a different way to report issues to you, but it seems this and Twitter are the only ways you can be reached, and I don't use twitter.