You really shouldn't need to use the configuration tool to start the game after the first time it is run. If you don't have stuff running in the background, etc, there also shouldn't be a huge variation in startup time.
Try uninstalling the game, make sure there are no files or folders left in the Divine Divinity folder, other than possibly the savegames folder, reboot, shut down all non-essential programs and reinstall the game. Try installing the game as administrator, and to a folder outside the default Program Files folder path (like c:\games, or something).
Each save is a separate subfolder in the '..\Divine Divinity\savegames' folder.
Under Vista/7, depending on how the user accounts are set up, if you install the game to the default Program Files path, Windows can create separate savegame folders for each user, and then map that folder to the game's savegame folder (so it will just see the saves for the relevant user).
C:\Users\ %account name% \AppData\Local\VirtualStore\Program Files\Divine Divinity\savegames
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Uncheck the 'Use AlphaBit' option unless you are having graphical problems in the game.
You can try switching to Software mode rather than Direct3D.
Are you shutting down all non-essential programs (especially anti-virus) before starting the game?
If you right click on the shortcut (or executable) for the game and select Properties, in the Compatibility tab you can disable desktop composition, etc, or set it to run in Win98/ME compatibility mode, and see if that helps.