We've had some problems with excessive logging in the past, but we thought we'd fixed them. The only thing we're aware of right now that might cause SQL Source Control to spit out loads of logs is if something's messing with the RedGate_SQLSourceControl_Engine_EngineOptions.xml in %LOCALAPPDATA%\\Red Gate\\SQL Source Control 3 - is it possible that you've got backup or antivirus software limiting access to that file? If SQL Source Control can't access it, it'll create a new one from scratch and log a lot of information.
Andy Campbell Smith
Red Gate Technical Support Engineer