Were you using beta 3.189 and before as the most recent? If so, then it's a matter of the old settings.dat file not being compatible with 4.0. When the game prompts you the first time, you want to import your old settings rather than saying begin fresh. Also, if you already hit begin fresh, you can run the importer from under the settings window of the game (button near the bottom of that window).
If you have your key in an email, though, that's all you need so you never have to buy it again. If you preordered from us, then steam doesn't have anything to do with it at the moment -- a bit confused. Hope that helps, but please clarify if not!