I did a search but couldn't find any info on how to start the game in Windows Mode. Here's how:

In the game install directory you will find the settings files defaults.ini and flux.ini. These files are in the same folder as the EdgeOfChaos.exe, goggame.dll etc.

If you open these files you will find under [FcGame] a line full_screen = 1. Change the 1 to a 0 in flux.ini and the game will run in windowed mode.

You can set the width/height to different resolutions. 800x600, 1024x768. I have it currently set to 1366x768. Dragging the window to re-size would probably create problems with game rendering. I haven't played the game yet---I have to get my joystick.

Hope this helps anyone wanting to play the game in window mode. :)

Windows 7 Ultimate (64-bit)