Ah! A -1 for OverallQuality is the Custom setting in the UI, which allows you to set your individual graphics settings to a mix of Low, Medium, or High. Low, Medium, and High Overall Quality are presets that force all of the other settings to the appropriate values. If you had Overall Quality set to one of those presets, that would explain why the game was always changing your settings back.
...and then suddenly you feel the power of simply logic slapping you in the face YeahBiotch! Makes perfect sense! =)
NoNeutrality - what are your system specs? I ask because with my low end system I have found the following settings have given me no performance hit over just running all low. I am so CPU bound it hurts. My resolution is for my monitor, but I have grown partial to a 1440x900 window as well. [Display] FullscreenRefresh=0 Maximized=0 FullscreenWidth=1920 FullscreenHeight=1080 WindowedWidth=1440 WindowedHeight=900 RenderQuality=1.000000 Mode=Fullscreen FullscreenMode=Fullscreen [Rendering] GraphicsQuality=3 TextureQuality=3 ShadowQuality=0 RenderDistance=2000 Gamma=0.000000 MaximumFPS=60 UseLod0a=0 OverallQuality=-1 LightingQuality=3 EffectsQuality=3 TerrainQuality=2 FloraQuality=0 ModelQuality=3 VerticalFOV=55 ParticleLOD=0 ParticleDistanceScale=0.650000 FogShadowsEnable=0 MotionBlur=0 VSync=0