Do you have any problems saving if you are not overwriting?
As a workaround, you could always increase the number of auto/quicksaves kept (in the Game options) and manually delete the oldest ones periodically.
Are you shutting down all non-essential programs (especially anti-virus) before starting the game?
Try starting the game directly from the '..\SteamApps\common\Divinity - Original Sin\Shipping\EoCApp.exe' program file, by right clicking and running as administrator.
If that doesn't help, please email supportdos@larian.com, with a description of the problem and the report.zip file generated by the
D:OS support tool.