You can try browsing to the '..\Documents\Larian Studios\Dragon Commander' folder and deleting or moving either the graphicSettings.lsx file or everything to get the game to recreate it the next time it is started. If the configuration files were not removed when you uninstalled the game (presumably the config files would be deleted and the saves kept), then there could be a difference between the game autodetecting settings on startup and getting them from the graphicSettings.lsx file.
Did you try running the game directly from the '..\SteamApps\common\Divinity Dragon Commander\Shipping\DCApp.exe' executable file, rather than through the Steam client?
If you don't have an anti-virus program or firewall, etc, running I'm not sure what else could make a difference from the first time the game was run...
Has there been a drop in performance with any other games, etc?
