Ah, this is a tricky one.
You need to do the following, which is basically removing your red, green and blue ini files from the steamcloud.
Given that you normally don't have access to this, a trick is required to get this done.
How to alter your steam cloud storage
1. Close steam (it cannot run!)
2. Use explorer to navigate to <steam>\userdata\##########\248190
3. Remove the file remotecache.vdf.
4. Open folder remote
5. Edit the red, green and blue ini files and delete all. (Each file becomes 0 bytes big)
6. Start steam.
7. Wait for it to finish synchronising.
8. If steam does not popup with a cloud storage conflict, launch the game to trigger the dialog.
9. Before doing anyhing, switch to your explorer window and remove the red, green and blue ini files.
10. Choose Copy local storage to cloud option.
11. This will delete the 3 files in the cloud as well.
12. The game should now run and start at the tutorial area.
Exit the game and as long as you don't complete the tutorial area, you'll start there.
If the above does not work, copy the settings file to a place outside the userdata folder and repeat the process, this time you include the settings.ini too. So when you trigger the sync conflict dialog, you delete everything in the remote folder, then choose copy to cloud.
The game will now launch full screen. Exit, and copy back the settings.ini. Because the cloud does not have a file there, it won't get overwritten on next launch.